--- /srv/rebuilderd/tmp/rebuilderdIREM2f/inputs/r-bioc-qusage_2.46.0-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdIREM2f/out/r-bioc-qusage_2.46.0-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-04 16:45:28.000000 debian-binary │ -rw-r--r-- 0 0 0 2116 2026-08-04 16:45:28.000000 control.tar.xz │ --rw-r--r-- 0 0 0 10232052 2026-08-04 16:45:28.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 10221300 2026-08-04 16:45:28.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./control │ │ │ @@ -1,12 +1,12 @@ │ │ │ Package: r-bioc-qusage │ │ │ Version: 2.46.0-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 10303 │ │ │ +Installed-Size: 10272 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-limma (>= 3.14), r-bioc-biobase, r-cran-nlme, r-cran-emmeans, r-cran-fftw, r-pkg-team-core-architecture │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/qusage/ │ │ │ Description: qusage: Quantitative Set Analysis for Gene Expression │ │ │ This package is an implementation the Quantitative Set │ │ │ Analysis for Gene Expression (QuSAGE) method described in │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -15,32 +15,32 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 561 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 481 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1868 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 197 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 692 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/NAMESPACE │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/qusage │ │ │ --rw-r--r-- 0 root (0) root (0) 189205 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/qusage.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1313 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/qusage.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 156426 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/qusage.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1307 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/R/qusage.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 68977 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/data/GeneSets.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 104 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/data/datalist │ │ │ -rw-r--r-- 0 root (0) root (0) 7863265 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/data/fluExample.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 981763 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/data/fluVaccine.RData │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1353 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 14466 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/doc/qusage.R │ │ │ -rw-r--r-- 0 root (0) root (0) 67007 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/doc/qusage.Rnw │ │ │ -rw-r--r-- 0 root (0) root (0) 1225543 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/doc/qusage.pdf │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 958 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 443 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 342 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/paths.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 76582 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/qusage.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 671 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/qusage.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 356 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 76876 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/qusage.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 673 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/help/qusage.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5758 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-04 16:45:28.000000 ./usr/lib/R/site-library/qusage/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 16:45:28.000000 ./usr/share/doc/r-bioc-qusage/ │ │ │ -rw-r--r-- 0 root (0) root (0) 801 2026-08-04 16:45:28.000000 ./usr/share/doc/r-bioc-qusage/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/qusage/R/qusage.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -624,15 +624,15 @@ │ │ │ │ "imports" = ""functionBody<-" = "functionBody<-", setLoadAction = "setLoadAction", " │ │ │ │ "imports" = ".__C__VIRTUAL = ".__C__VIRTUAL", superClassDepth = "superClassDepth", " │ │ │ │ "imports" = ".__C__SClassExtension = ".__C__SClassExtension", existsMethod = "existsMethod", " │ │ │ │ "imports" = "getFunction = "getFunction", getMethodsMetaData = "getMethodsMetaData"" │ │ │ │ "imports" = "), fftw = c(IFFT = "IFFT", DCT = "DCT", FFT = "FFT", IDCT = "IDCT", " │ │ │ │ "imports" = "planDCT = "planDCT", planFFT = "planFFT"), graphics = c(plot = "plot"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-qusage/debian/tmp/usr/lib/R/site-library/qusage"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-qusage-2.46.0/debian/tmp/usr/lib/R/site-library/qusage"" │ │ │ │ "spec" = "c(name = "qusage", version = "2.46.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ │ │ │ │ │ │ @@ -648,71 +648,20 @@ │ │ │ │ │ │ │ │ .__T__head:utils (environment) = │ │ │ │ { │ │ │ │ "ANY" = "new("derivedDefaultMethod", .Data = function (x, ...) " │ │ │ │ "ANY" = "UseMethod("head"), target = new("signature", .Data = "ANY", names = "x", " │ │ │ │ "ANY" = " package = "methods"), defined = new("signature", .Data = "ANY", " │ │ │ │ "ANY" = " names = "x", package = "methods"), generic = structure("head", package = "utils"))" │ │ │ │ - "Matrix" = "new("MethodDefinition", .Data = function (x, ...) " │ │ │ │ - "Matrix" = "{" │ │ │ │ - "Matrix" = " .local <- function (x, n = 6L, ...) " │ │ │ │ - "Matrix" = " {" │ │ │ │ - "Matrix" = " .checkHT(n, d <- dim(x))" │ │ │ │ - "Matrix" = " args <- rep(alist(x, , drop = FALSE), c(1L, length(d), " │ │ │ │ - "Matrix" = " 1L))" │ │ │ │ - "Matrix" = " ii <- which(!is.na(n[seq_along(d)]))" │ │ │ │ - "Matrix" = " args[1L + ii] <- lapply(ii, function(i) seq_len(if ((ni <- n[i]) < " │ │ │ │ - "Matrix" = " 0L) max(d[i] + ni, 0L) else min(ni, d[i])))" │ │ │ │ - "Matrix" = " do.call(`[`, args)" │ │ │ │ - "Matrix" = " }" │ │ │ │ - "Matrix" = " .local(x, ...)" │ │ │ │ - "Matrix" = "}, target = new("signature", .Data = "Matrix", names = "x", package = "Matrix"), " │ │ │ │ - "Matrix" = " defined = new("signature", .Data = "Matrix", names = "x", " │ │ │ │ - "Matrix" = " package = "Matrix"), generic = structure("head", package = "utils"))" │ │ │ │ "QSarray" = "new("MethodDefinition", .Data = function (x, ...) " │ │ │ │ "QSarray" = "{" │ │ │ │ "QSarray" = " invisible(print(x))" │ │ │ │ "QSarray" = "}, target = new("signature", .Data = "QSarray", names = "x", " │ │ │ │ "QSarray" = " package = "qusage"), defined = new("signature", .Data = "QSarray", " │ │ │ │ "QSarray" = " names = "x", package = "qusage"), generic = structure("head", package = "utils"))" │ │ │ │ - "sparseVector" = "new("MethodDefinition", .Data = function (x, ...) " │ │ │ │ - "sparseVector" = "{" │ │ │ │ - "sparseVector" = " .local <- function (x, n = 6L, ...) " │ │ │ │ - "sparseVector" = " {" │ │ │ │ - "sparseVector" = " stopifnot(is.numeric(n), length(n) == 1L, !is.na(n))" │ │ │ │ - "sparseVector" = " len <- length(x)" │ │ │ │ - "sparseVector" = " n <- if (n < 0L) " │ │ │ │ - "sparseVector" = " max(len + n, 0L)" │ │ │ │ - "sparseVector" = " else min(n, len)" │ │ │ │ - "sparseVector" = " if (n >= len) " │ │ │ │ - "sparseVector" = " return(x)" │ │ │ │ - "sparseVector" = " nnz <- length(i <- x@i)" │ │ │ │ - "sparseVector" = " x@length <- n <- if (is.integer(i)) " │ │ │ │ - "sparseVector" = " as.integer(n)" │ │ │ │ - "sparseVector" = " else trunc(n)" │ │ │ │ - "sparseVector" = " if (nnz > 0L && i[nnz] > n) {" │ │ │ │ - "sparseVector" = " pattern <- .M.kind(x) == "n"" │ │ │ │ - "sparseVector" = " if (i[1L] > n) {" │ │ │ │ - "sparseVector" = " x@i <- integer(0L)" │ │ │ │ - "sparseVector" = " if (!pattern) " │ │ │ │ - "sparseVector" = " x@x <- x@x[0L]" │ │ │ │ - "sparseVector" = " }" │ │ │ │ - "sparseVector" = " else {" │ │ │ │ - "sparseVector" = " ii <- 1L:(which.max(i > n) - 1L)" │ │ │ │ - "sparseVector" = " x@i <- i[ii]" │ │ │ │ - "sparseVector" = " if (!pattern) " │ │ │ │ - "sparseVector" = " x@x <- x@x[ii]" │ │ │ │ - "sparseVector" = " }" │ │ │ │ - "sparseVector" = " }" │ │ │ │ - "sparseVector" = " x" │ │ │ │ - "sparseVector" = " }" │ │ │ │ - "sparseVector" = " .local(x, ...)" │ │ │ │ - "sparseVector" = "}, target = new("signature", .Data = "sparseVector", names = "x", " │ │ │ │ - "sparseVector" = " package = "Matrix"), defined = new("signature", .Data = "sparseVector", " │ │ │ │ - "sparseVector" = " names = "x", package = "Matrix"), generic = structure("head", package = "utils"))" │ │ │ │ } │ │ │ │ │ │ │ │ .__T__numFeatures:qusage (environment) = │ │ │ │ { │ │ │ │ "QSarray" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "QSarray" = "{" │ │ │ │ "QSarray" = " genes = NA" │ │ │ │ @@ -815,134 +764,14 @@ │ │ │ │ "QSarray" = " }" │ │ │ │ "QSarray" = " }" │ │ │ │ "QSarray" = " }" │ │ │ │ "QSarray" = " invisible(x)" │ │ │ │ "QSarray" = "}, target = new("signature", .Data = "QSarray", names = "x", " │ │ │ │ "QSarray" = " package = "qusage"), defined = new("signature", .Data = "QSarray", " │ │ │ │ "QSarray" = " names = "x", package = "qusage"), generic = structure("print", package = "base"))" │ │ │ │ - "diagonalMatrix" = "new("MethodDefinition", .Data = function (x, ...) " │ │ │ │ - "diagonalMatrix" = "{" │ │ │ │ - "diagonalMatrix" = " .local <- function (x, digits = getOption("digits"), justify = "none", " │ │ │ │ - "diagonalMatrix" = " right = TRUE, ...) " │ │ │ │ - "diagonalMatrix" = " {" │ │ │ │ - "diagonalMatrix" = " cf <- array(".", dim = x@Dim, dimnames = x@Dimnames)" │ │ │ │ - "diagonalMatrix" = " cf[row(cf) == col(cf)] <- vapply(diag(x), format, "", " │ │ │ │ - "diagonalMatrix" = " digits = digits, justify = justify)" │ │ │ │ - "diagonalMatrix" = " print(cf, quote = FALSE, right = right)" │ │ │ │ - "diagonalMatrix" = " invisible(x)" │ │ │ │ - "diagonalMatrix" = " }" │ │ │ │ - "diagonalMatrix" = " .local(x, ...)" │ │ │ │ - "diagonalMatrix" = "}, target = new("signature", .Data = "diagonalMatrix", names = "x", " │ │ │ │ - "diagonalMatrix" = " package = "Matrix"), defined = new("signature", .Data = "diagonalMatrix", " │ │ │ │ - "diagonalMatrix" = " names = "x", package = "Matrix"), generic = structure("print", package = "base"))" │ │ │ │ - "sparseMatrix" = "new("MethodDefinition", .Data = function (x, ...) " │ │ │ │ - "sparseMatrix" = "{" │ │ │ │ - "sparseMatrix" = " .local <- function (x, digits = NULL, maxp = max(100L, getOption("max.print")), " │ │ │ │ - "sparseMatrix" = " zero.print = ".", col.names, note.dropping.colnames = TRUE, " │ │ │ │ - "sparseMatrix" = " uniDiag = TRUE, suppRows = NULL, suppCols = NULL, col.trailer = if (suppCols) " │ │ │ │ - "sparseMatrix" = " "......"" │ │ │ │ - "sparseMatrix" = " else "", align = c("fancy", "right"), width = getOption("width"), " │ │ │ │ - "sparseMatrix" = " fitWidth = TRUE, ...) " │ │ │ │ - "sparseMatrix" = " {" │ │ │ │ - "sparseMatrix" = " d <- dim(x)" │ │ │ │ - "sparseMatrix" = " cl <- class(x)" │ │ │ │ - "sparseMatrix" = " cld <- getClassDef(cl)" │ │ │ │ - "sparseMatrix" = " xtra <- if (extends(cld, "triangularMatrix") && x@diag == " │ │ │ │ - "sparseMatrix" = " "U") " │ │ │ │ - "sparseMatrix" = " " (unitriangular)"" │ │ │ │ - "sparseMatrix" = " else """ │ │ │ │ - "sparseMatrix" = " cat(sprintf("%d x %d sparse Matrix of class \"%s\"%s\n", " │ │ │ │ - "sparseMatrix" = " d[1], d[2], cl, xtra))" │ │ │ │ - "sparseMatrix" = " setW <- !missing(width) && width > getOption("width")" │ │ │ │ - "sparseMatrix" = " if (setW) {" │ │ │ │ - "sparseMatrix" = " op <- options(width = width)" │ │ │ │ - "sparseMatrix" = " on.exit(options(op))" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " if ((isFALSE(suppRows) && isFALSE(suppCols)) || (!isTRUE(suppRows) && " │ │ │ │ - "sparseMatrix" = " !isTRUE(suppCols) && prod(d) <= maxp)) {" │ │ │ │ - "sparseMatrix" = " if (missing(col.trailer) && is.null(suppCols)) " │ │ │ │ - "sparseMatrix" = " suppCols <- FALSE" │ │ │ │ - "sparseMatrix" = " printSpMatrix(x, cld = cld, digits = digits, maxp = maxp, " │ │ │ │ - "sparseMatrix" = " zero.print = zero.print, col.names = col.names, " │ │ │ │ - "sparseMatrix" = " note.dropping.colnames = note.dropping.colnames, " │ │ │ │ - "sparseMatrix" = " uniDiag = uniDiag, col.trailer = col.trailer, " │ │ │ │ - "sparseMatrix" = " align = align)" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " else {" │ │ │ │ - "sparseMatrix" = " validObject(x)" │ │ │ │ - "sparseMatrix" = " sTxt <- c(" ", gettext("in show(); maybe adjust options(max.print=, width=)"), " │ │ │ │ - "sparseMatrix" = " "\n ..............................\n")" │ │ │ │ - "sparseMatrix" = " useW <- width - (format.info(d[1], digits = digits)[1] + " │ │ │ │ - "sparseMatrix" = " 3 + 1)" │ │ │ │ - "sparseMatrix" = " if (is.null(suppCols)) " │ │ │ │ - "sparseMatrix" = " suppCols <- (d[2] * 2 > useW)" │ │ │ │ - "sparseMatrix" = " nCc <- 1 + nchar(col.trailer, "width")" │ │ │ │ - "sparseMatrix" = " if (suppCols) {" │ │ │ │ - "sparseMatrix" = " nc <- (useW - nCc)%/%2" │ │ │ │ - "sparseMatrix" = " x <- x[, 1:nc, drop = FALSE]" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " else nc <- d[2]" │ │ │ │ - "sparseMatrix" = " nr <- maxp%/%nc" │ │ │ │ - "sparseMatrix" = " if (is.null(suppRows)) " │ │ │ │ - "sparseMatrix" = " suppRows <- (nr < d[1])" │ │ │ │ - "sparseMatrix" = " if (suppRows) {" │ │ │ │ - "sparseMatrix" = " n2 <- ceiling(nr/2)" │ │ │ │ - "sparseMatrix" = " nr1 <- min(d[1], max(1L, n2))" │ │ │ │ - "sparseMatrix" = " nr2 <- max(1L, nr - n2)" │ │ │ │ - "sparseMatrix" = " nr <- nr1 + nr2" │ │ │ │ - "sparseMatrix" = " if (fitWidth) {" │ │ │ │ - "sparseMatrix" = " cM <- formatSpMatrix(x[seq_len(nr1), , drop = FALSE], " │ │ │ │ - "sparseMatrix" = " digits = digits, maxp = maxp, zero.print = zero.print, " │ │ │ │ - "sparseMatrix" = " col.names = col.names, align = align, note.dropping.colnames = note.dropping.colnames, " │ │ │ │ - "sparseMatrix" = " uniDiag = FALSE)" │ │ │ │ - "sparseMatrix" = " matW <- nchar(capture.output(print(cM, quote = FALSE, " │ │ │ │ - "sparseMatrix" = " right = FALSE))[[1]])" │ │ │ │ - "sparseMatrix" = " needW <- matW + (if (suppCols) " │ │ │ │ - "sparseMatrix" = " nCc" │ │ │ │ - "sparseMatrix" = " else 0)" │ │ │ │ - "sparseMatrix" = " if (needW > useW) {" │ │ │ │ - "sparseMatrix" = " op <- options(width = width + (needW - useW))" │ │ │ │ - "sparseMatrix" = " if (!setW) " │ │ │ │ - "sparseMatrix" = " on.exit(options(op))" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " printSpMatrix(x[seq_len(nr1), , drop = FALSE], " │ │ │ │ - "sparseMatrix" = " digits = digits, maxp = maxp, zero.print = zero.print, " │ │ │ │ - "sparseMatrix" = " col.names = col.names, note.dropping.colnames = note.dropping.colnames, " │ │ │ │ - "sparseMatrix" = " uniDiag = uniDiag, col.trailer = col.trailer, " │ │ │ │ - "sparseMatrix" = " align = align)" │ │ │ │ - "sparseMatrix" = " suppTxt <- if (suppCols) " │ │ │ │ - "sparseMatrix" = " gettextf("suppressing %d columns and %d rows", " │ │ │ │ - "sparseMatrix" = " d[2] - nc, d[1] - nr)" │ │ │ │ - "sparseMatrix" = " else gettextf("suppressing %d rows", d[1] - nr)" │ │ │ │ - "sparseMatrix" = " cat("\n ..............................", "\n ........", " │ │ │ │ - "sparseMatrix" = " suppTxt, sTxt, sep = "")" │ │ │ │ - "sparseMatrix" = " printSpMatrix(tail(x, nr2), digits = digits, " │ │ │ │ - "sparseMatrix" = " maxp = maxp, zero.print = zero.print, col.names = col.names, " │ │ │ │ - "sparseMatrix" = " note.dropping.colnames = note.dropping.colnames, " │ │ │ │ - "sparseMatrix" = " uniDiag = FALSE, col.trailer = col.trailer, " │ │ │ │ - "sparseMatrix" = " align = align)" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " else if (suppCols) {" │ │ │ │ - "sparseMatrix" = " printSpMatrix(x[, 1:nc, drop = FALSE], digits = digits, " │ │ │ │ - "sparseMatrix" = " maxp = maxp, zero.print = zero.print, col.names = col.names, " │ │ │ │ - "sparseMatrix" = " note.dropping.colnames = note.dropping.colnames, " │ │ │ │ - "sparseMatrix" = " uniDiag = uniDiag, col.trailer = col.trailer, " │ │ │ │ - "sparseMatrix" = " align = align)" │ │ │ │ - "sparseMatrix" = " cat("\n .....", gettextf("suppressing %d columns", " │ │ │ │ - "sparseMatrix" = " d[2] - nc), sTxt, sep = "")" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " else stop("logic programming error in printSpMatrix2(), please report")" │ │ │ │ - "sparseMatrix" = " invisible(x)" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " .local(x, ...)" │ │ │ │ - "sparseMatrix" = "}, target = new("signature", .Data = "sparseMatrix", names = "x", " │ │ │ │ - "sparseMatrix" = " package = "Matrix"), defined = new("signature", .Data = "sparseMatrix", " │ │ │ │ - "sparseMatrix" = " names = "x", package = "Matrix"), generic = structure("print", package = "base"))" │ │ │ │ } │ │ │ │ │ │ │ │ .__T__summary:base (environment) = │ │ │ │ { │ │ │ │ "ANY" = "new("derivedDefaultMethod", .Data = function (object, ...) " │ │ │ │ "ANY" = "UseMethod("summary"), target = new("signature", .Data = "ANY", " │ │ │ │ "ANY" = " names = "object", package = "methods"), defined = new("signature", " │ │ │ │ @@ -957,40 +786,14 @@ │ │ │ │ "QSarray" = " }" │ │ │ │ "QSarray" = " else {" │ │ │ │ "QSarray" = " return(qsTable(object))" │ │ │ │ "QSarray" = " }" │ │ │ │ "QSarray" = "}, target = new("signature", .Data = "QSarray", names = "object", " │ │ │ │ "QSarray" = " package = "qusage"), defined = new("signature", .Data = "QSarray", " │ │ │ │ "QSarray" = " names = "object", package = "qusage"), generic = structure("summary", package = "base"))" │ │ │ │ - "diagonalMatrix" = "new("MethodDefinition", .Data = function (object, ...) " │ │ │ │ - "diagonalMatrix" = "{" │ │ │ │ - "diagonalMatrix" = " d <- object@Dim" │ │ │ │ - "diagonalMatrix" = " r <- summary(object@x, ...)" │ │ │ │ - "diagonalMatrix" = " attr(r, "header") <- sprintf("%d x %d diagonal Matrix of class \"%s\"", " │ │ │ │ - "diagonalMatrix" = " d[1L], d[2L], class(object))" │ │ │ │ - "diagonalMatrix" = " class(r) <- c("diagSummary", class(r))" │ │ │ │ - "diagonalMatrix" = " r" │ │ │ │ - "diagonalMatrix" = "}, target = new("signature", .Data = "diagonalMatrix", names = "object", " │ │ │ │ - "diagonalMatrix" = " package = "Matrix"), defined = new("signature", .Data = "diagonalMatrix", " │ │ │ │ - "diagonalMatrix" = " names = "object", package = "Matrix"), generic = structure("summary", package = "base"))" │ │ │ │ - "sparseMatrix" = "new("MethodDefinition", .Data = function (object, ...) " │ │ │ │ - "sparseMatrix" = "{" │ │ │ │ - "sparseMatrix" = " .local <- function (object, uniqT = FALSE, ...) " │ │ │ │ - "sparseMatrix" = " {" │ │ │ │ - "sparseMatrix" = " d <- object@Dim" │ │ │ │ - "sparseMatrix" = " r <- as.data.frame(mat2triplet(object, uniqT = uniqT))" │ │ │ │ - "sparseMatrix" = " attr(r, "header") <- sprintf("%d x %d sparse Matrix of class \"%s\", with %d entries", " │ │ │ │ - "sparseMatrix" = " d[1L], d[2L], class(object), nrow(r))" │ │ │ │ - "sparseMatrix" = " class(r) <- c("sparseSummary", oldClass(r))" │ │ │ │ - "sparseMatrix" = " r" │ │ │ │ - "sparseMatrix" = " }" │ │ │ │ - "sparseMatrix" = " .local(object, ...)" │ │ │ │ - "sparseMatrix" = "}, target = new("signature", .Data = "sparseMatrix", names = "object", " │ │ │ │ - "sparseMatrix" = " package = "Matrix"), defined = new("signature", .Data = "sparseMatrix", " │ │ │ │ - "sparseMatrix" = " names = "object", package = "Matrix"), generic = structure("summary", package = "base"))" │ │ │ │ } │ │ │ │ │ │ │ │ .packageName (character) = "qusage" │ │ │ │ │ │ │ │ .requireCachedGenerics (list) = structure(list("Ops"), package = "base") │ │ │ │ │ │ │ │ Ni (closure) = function (SigmaOld, SigmaYoung, NOld, NYoung) │ │ ├── ./usr/lib/R/site-library/qusage/R/qusage.rdx │ │ │ ├── qusage.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,268 +1,268 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__C__QSarray │ │ │ │ │ [1] 0 1443 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 11684 52 │ │ │ │ │ +[1] 11688 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 11867 52 │ │ │ │ │ +[1] 11871 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__dim:base` │ │ │ │ │ -[1] 14651 52 │ │ │ │ │ +[1] 14413 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__head:utils` │ │ │ │ │ -[1] 26343 52 │ │ │ │ │ +[1] 16556 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__numFeatures:qusage` │ │ │ │ │ -[1] 28769 53 │ │ │ │ │ +[1] 18982 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__numPathways:qusage` │ │ │ │ │ -[1] 31918 53 │ │ │ │ │ +[1] 22131 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__plot:base` │ │ │ │ │ -[1] 35971 53 │ │ │ │ │ +[1] 26184 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__print:base` │ │ │ │ │ -[1] 61515 53 │ │ │ │ │ +[1] 32090 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__summary:base` │ │ │ │ │ -[1] 68356 53 │ │ │ │ │ +[1] 35577 53 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 68409 51 │ │ │ │ │ +[1] 35630 51 │ │ │ │ │ │ │ │ │ │ $variables$.requireCachedGenerics │ │ │ │ │ -[1] 68460 75 │ │ │ │ │ +[1] 35681 75 │ │ │ │ │ │ │ │ │ │ $variables$Ni │ │ │ │ │ -[1] 68535 541 │ │ │ │ │ +[1] 35756 541 │ │ │ │ │ │ │ │ │ │ $variables$absoluteTest │ │ │ │ │ -[1] 69076 1937 │ │ │ │ │ +[1] 36297 1937 │ │ │ │ │ │ │ │ │ │ $variables$absoluteTest.genePvals │ │ │ │ │ -[1] 71013 5655 │ │ │ │ │ +[1] 38234 5655 │ │ │ │ │ │ │ │ │ │ $variables$absoluteTest.genePvalsFAST │ │ │ │ │ -[1] 76668 1957 │ │ │ │ │ +[1] 43889 1957 │ │ │ │ │ │ │ │ │ │ $variables$aggregateGeneSet │ │ │ │ │ -[1] 78625 5319 │ │ │ │ │ +[1] 45846 5319 │ │ │ │ │ │ │ │ │ │ $variables$approximatedNu │ │ │ │ │ -[1] 83944 2012 │ │ │ │ │ +[1] 51165 2012 │ │ │ │ │ │ │ │ │ │ $variables$calcBayesCI │ │ │ │ │ -[1] 85956 2301 │ │ │ │ │ +[1] 53177 2301 │ │ │ │ │ │ │ │ │ │ $variables$calcIndividualExpressions │ │ │ │ │ -[1] 88257 4191 │ │ │ │ │ +[1] 55478 4191 │ │ │ │ │ │ │ │ │ │ $variables$calcPCor │ │ │ │ │ -[1] 92448 4554 │ │ │ │ │ +[1] 59669 4554 │ │ │ │ │ │ │ │ │ │ $variables$calcVIF │ │ │ │ │ -[1] 97002 4575 │ │ │ │ │ +[1] 64223 4575 │ │ │ │ │ │ │ │ │ │ $variables$calculate_bayesGHelper │ │ │ │ │ -[1] 101577 965 │ │ │ │ │ +[1] 68798 965 │ │ │ │ │ │ │ │ │ │ $variables$combinePDFs │ │ │ │ │ -[1] 102542 5676 │ │ │ │ │ +[1] 69763 5676 │ │ │ │ │ │ │ │ │ │ $variables$compareTwoDistsFaster │ │ │ │ │ -[1] 108218 1258 │ │ │ │ │ +[1] 75439 1258 │ │ │ │ │ │ │ │ │ │ $variables$filterGenes │ │ │ │ │ -[1] 109476 945 │ │ │ │ │ +[1] 76697 945 │ │ │ │ │ │ │ │ │ │ $variables$getExAbs │ │ │ │ │ -[1] 110421 470 │ │ │ │ │ +[1] 77642 470 │ │ │ │ │ │ │ │ │ │ $variables$getXcoords │ │ │ │ │ -[1] 110891 1098 │ │ │ │ │ +[1] 78112 1098 │ │ │ │ │ │ │ │ │ │ $variables$head │ │ │ │ │ -[1] 111989 451 │ │ │ │ │ +[1] 79210 451 │ │ │ │ │ │ │ │ │ │ $variables$homogeneityScore │ │ │ │ │ -[1] 112440 1206 │ │ │ │ │ +[1] 79661 1206 │ │ │ │ │ │ │ │ │ │ $variables$makeComparison │ │ │ │ │ -[1] 113646 5574 │ │ │ │ │ +[1] 80867 5574 │ │ │ │ │ │ │ │ │ │ $variables$multi_conv │ │ │ │ │ -[1] 119220 1440 │ │ │ │ │ +[1] 86441 1440 │ │ │ │ │ │ │ │ │ │ $variables$newQSarray │ │ │ │ │ -[1] 120660 1833 │ │ │ │ │ +[1] 87881 1833 │ │ │ │ │ │ │ │ │ │ $variables$nonsingular.check │ │ │ │ │ -[1] 122493 357 │ │ │ │ │ +[1] 89714 357 │ │ │ │ │ │ │ │ │ │ $variables$numFeatures │ │ │ │ │ -[1] 122850 397 │ │ │ │ │ +[1] 90071 397 │ │ │ │ │ │ │ │ │ │ $variables$numPathways │ │ │ │ │ -[1] 123247 399 │ │ │ │ │ +[1] 90468 399 │ │ │ │ │ │ │ │ │ │ $variables$oneWay.pVal │ │ │ │ │ -[1] 123646 492 │ │ │ │ │ +[1] 90867 492 │ │ │ │ │ │ │ │ │ │ $variables$pdf.pVal │ │ │ │ │ -[1] 124138 3356 │ │ │ │ │ +[1] 91359 3356 │ │ │ │ │ │ │ │ │ │ $variables$pdfScaleFactor │ │ │ │ │ -[1] 127494 1234 │ │ │ │ │ +[1] 94715 1234 │ │ │ │ │ │ │ │ │ │ $variables$plot │ │ │ │ │ -[1] 128728 446 │ │ │ │ │ +[1] 95949 446 │ │ │ │ │ │ │ │ │ │ $variables$plotCIs │ │ │ │ │ -[1] 129174 9827 │ │ │ │ │ +[1] 96395 9827 │ │ │ │ │ │ │ │ │ │ $variables$plotCIsGenes │ │ │ │ │ -[1] 139001 8043 │ │ │ │ │ +[1] 106222 8043 │ │ │ │ │ │ │ │ │ │ $variables$plotCombinedPDF │ │ │ │ │ -[1] 147044 5116 │ │ │ │ │ +[1] 114265 5116 │ │ │ │ │ │ │ │ │ │ $variables$plotDensityCurves │ │ │ │ │ -[1] 152160 2908 │ │ │ │ │ +[1] 119381 2908 │ │ │ │ │ │ │ │ │ │ $variables$plotGeneSetDistributions │ │ │ │ │ -[1] 155068 12339 │ │ │ │ │ +[1] 122289 12339 │ │ │ │ │ │ │ │ │ │ $variables$print │ │ │ │ │ -[1] 167407 434 │ │ │ │ │ +[1] 134628 434 │ │ │ │ │ │ │ │ │ │ $variables$qgen │ │ │ │ │ -[1] 167841 9956 │ │ │ │ │ +[1] 135062 9956 │ │ │ │ │ │ │ │ │ │ $variables$qsTable │ │ │ │ │ -[1] 177797 1656 │ │ │ │ │ +[1] 145018 1656 │ │ │ │ │ │ │ │ │ │ $variables$qusage │ │ │ │ │ -[1] 179453 2360 │ │ │ │ │ +[1] 146674 2360 │ │ │ │ │ │ │ │ │ │ $variables$qusage.single │ │ │ │ │ -[1] 181813 1145 │ │ │ │ │ +[1] 149034 1145 │ │ │ │ │ │ │ │ │ │ $variables$read.gmt │ │ │ │ │ -[1] 182958 1043 │ │ │ │ │ +[1] 150179 1043 │ │ │ │ │ │ │ │ │ │ $variables$summary │ │ │ │ │ -[1] 184001 440 │ │ │ │ │ +[1] 151222 440 │ │ │ │ │ │ │ │ │ │ $variables$twoCurve.pVal │ │ │ │ │ -[1] 184441 2293 │ │ │ │ │ +[1] 151662 2293 │ │ │ │ │ │ │ │ │ │ $variables$twoWay.pVal │ │ │ │ │ -[1] 186734 573 │ │ │ │ │ +[1] 153955 573 │ │ │ │ │ │ │ │ │ │ $variables$weighted_conv │ │ │ │ │ -[1] 187307 1898 │ │ │ │ │ +[1] 154528 1898 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 1731 9953 │ │ │ │ │ +[1] 1731 9957 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 22181 423 │ │ │ │ │ +[1] 15577 423 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 14703 3739 │ │ │ │ │ +[1] 14465 556 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 18442 3739 │ │ │ │ │ +[1] 15021 556 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 28064 705 │ │ │ │ │ +[1] 18277 705 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 27805 259 │ │ │ │ │ +[1] 18018 259 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 26395 705 │ │ │ │ │ +[1] 16608 705 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 27100 705 │ │ │ │ │ +[1] 17313 705 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 30973 945 │ │ │ │ │ +[1] 21186 945 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 30712 261 │ │ │ │ │ +[1] 20925 261 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 28822 945 │ │ │ │ │ +[1] 19035 945 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 1443 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 29767 945 │ │ │ │ │ +[1] 19980 945 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 34776 1195 │ │ │ │ │ +[1] 24989 1195 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 34361 415 │ │ │ │ │ +[1] 24574 415 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 31971 1195 │ │ │ │ │ +[1] 22184 1195 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 33166 1195 │ │ │ │ │ +[1] 23379 1195 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 53155 8360 │ │ │ │ │ +[1] 30276 1814 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 52744 411 │ │ │ │ │ +[1] 29865 411 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 36024 8360 │ │ │ │ │ +[1] 26237 1814 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 44384 8360 │ │ │ │ │ +[1] 28051 1814 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 66232 2124 │ │ │ │ │ +[1] 34571 1006 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 1574 157 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 65816 416 │ │ │ │ │ +[1] 34155 416 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 61568 2124 │ │ │ │ │ +[1] 32143 1006 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 63692 2124 │ │ │ │ │ +[1] 33149 1006 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 11736 131 │ │ │ │ │ +[1] 11740 131 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 14156 495 │ │ │ │ │ +[1] 13918 495 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 13901 255 │ │ │ │ │ +[1] 13663 255 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 11919 991 │ │ │ │ │ +[1] 11923 870 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 12910 991 │ │ │ │ │ +[1] 12793 870 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 22604 3739 │ │ │ │ │ +[1] 16000 556 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/qusage/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,23 +1,23 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-qusage/man/GeneSets.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-qusage/man/QSarray-class.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-qusage/man/aggregateGeneSet.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-qusage/man/calcBayesCI.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-qusage/man/calcVIF.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-qusage/man/combinePDFs.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-qusage/man/eset.full.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-qusage/man/fluVaccine.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-qusage/man/getXcoords.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-qusage/man/makeComparison.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-qusage/man/newQSarray.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-qusage/man/pVal.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-qusage/man/plotCIs.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-qusage/man/plotCIsGenes.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-qusage/man/plotCombinedPDF.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-qusage/man/plotDensityCurves.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-qusage/man/plotGeneSetDistributions.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-qusage/man/qgen.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-qusage/man/qsTable.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-qusage/man/qusage.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-qusage/man/read.gmt.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/GeneSets.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/QSarray-class.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/aggregateGeneSet.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/calcBayesCI.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/calcVIF.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/combinePDFs.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/eset.full.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/fluVaccine.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/getXcoords.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/makeComparison.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/newQSarray.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/pVal.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCIs.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCIsGenes.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCombinedPDF.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotDensityCurves.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotGeneSetDistributions.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qgen.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qsTable.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qusage.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-qusage-2.46.0/man/read.gmt.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 39 │ │ │ │ │ +[1] 51 │ │ ├── ./usr/lib/R/site-library/qusage/help/qusage.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -18,15 +18,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" ISG.geneSet\n", Rd_tag = "RCODE"), │ │ │ │ structure(" MSIG.geneSets\n", Rd_tag = "RCODE"), structure(" BTM.geneSet\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure(list(structure("http://www.broadinstitute.org/gsea/msigdb/", Rd_tag = "VERB")), Rd_tag = "\\url")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ISG: Schoggins et al. (Nature, 2011).\n", Rd_tag = "TEXT"), │ │ │ │ structure(" \n", Rd_tag = "TEXT"), structure(" MSIG: Liberzon et al. (Bioinformatics, 2011)\n", Rd_tag = "TEXT"), │ │ │ │ - structure(" \n", Rd_tag = "TEXT"), structure(" BTM: Li et al. (Nat Immunol., 2014).\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/GeneSets.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "TEXT"), structure(" BTM: Li et al. (Nat Immunol., 2014).\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/GeneSets.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ QSarray-class (list) = structure(list(structure(list(structure("Class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("\"QSarray\"", Rd_tag = "RCODE")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("QSarray-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("QSarray-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("dim,QSarray-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -211,15 +211,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("qsTable", Rd_tag = "TEXT")), │ │ │ │ list(structure("Print a table with a summary of the information on the most significant gene sets in QSarray. See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("qsTable", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" for more details.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Christopher Bolen\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/QSarray-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Christopher Bolen\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/QSarray-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ aggregateGeneSet (list) = structure(list(structure(list(structure("Calculate Pathway Activation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("aggregateGeneSet", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("aggregateGeneSet", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Combine individual gene differential expresseion for each pathway\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -271,15 +271,15 @@ │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##first 30 genes are differentially expressed\n", Rd_tag = "RCODE"), │ │ │ │ structure(" eset[1:30, labels==\"B\"] = eset[1:30, labels==\"B\"] + 1\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##compare the two groups\n", Rd_tag = "RCODE"), │ │ │ │ structure(" geneResults = makeComparison(eset, labels, \"B-A\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##aggregate data for gene sets\n", Rd_tag = "RCODE"), │ │ │ │ structure(" geneSets = list(set1=1:30, set2=31:60)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" set.results = aggregateGeneSet(geneResults, geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/aggregateGeneSet.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/aggregateGeneSet.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ calcBayesCI (list) = structure(list(structure(list(structure("Calculate pathway Confidence Intervals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcBayesCI", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcBayesCI", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A function to calculate the confidence intervals for each of the gene sets in the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("geneResults", Rd_tag = "TEXT")), Rd_tag = "\\var"), │ │ │ │ @@ -307,15 +307,15 @@ │ │ │ │ structure(list(structure("plotCIs", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure(" to plot the confidence intervals of each pathway.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Matrix of size (", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("2 x numPathways(QSarray)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(") containing the lower and upper bounds of the confidence intervals for each pathway in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("QSarray", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ - structure(".\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/calcBayesCI.Rd", class = "Rd", meta = list( │ │ │ │ + structure(".\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/calcBayesCI.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ calcVIF (list) = structure(list(structure(list(structure("Calculate Variance Inflation Factor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcVIF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcVIF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A function to calculate the Variance Inflation Factor (VIF) for each of the gene sets in the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("geneResults", Rd_tag = "TEXT")), Rd_tag = "\\var"), │ │ │ │ @@ -399,15 +399,15 @@ │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##calc VIF for gene sets\n", Rd_tag = "RCODE"), │ │ │ │ structure(" set.results = calcVIF(eset, set.results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##Look at results with and without VIF\n", Rd_tag = "RCODE"), │ │ │ │ structure(" par(mfrow=c(1,2))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotDensityCurves(set.results, addVIF=FALSE, col=1:2, main=\"No VIF\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotDensityCurves(set.results, addVIF=TRUE, col=1:2, main=\"With VIF\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" legend(\"topleft\",legend=names(geneSets),col=1:2, lty=1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/calcVIF.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/calcVIF.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ combinePDFs (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Combine PDFs from multiple QuSAGE comparisons\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("combinePDFs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("combinePDFs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function combines the results of multiple ", Rd_tag = "TEXT"), │ │ │ │ @@ -447,15 +447,15 @@ │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##calculate qusage results\n", Rd_tag = "RCODE"), │ │ │ │ structure(" qsList = lapply(c(\"B-A\",\"D-C\"), function(comparison){\n", Rd_tag = "RCODE"), │ │ │ │ structure(" qusage(eset,labels, comparison, geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" })\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure("##combine the two QSarrays\n", Rd_tag = "RCODE"), │ │ │ │ structure(" qsComb = combinePDFs(qsList)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" plot(qsComb, path.index=1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/combinePDFs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" plot(qsComb, path.index=1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/combinePDFs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ eset.full (list) = structure(list(structure(list(structure("Example gene expression set", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fluExample", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fluExample", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("eset.full", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("flu.meta", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -493,15 +493,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" eset.full\n", Rd_tag = "RCODE"), │ │ │ │ structure(" flu.meta\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure(list(structure("eset.full", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is a matrix of gene expression measurements, with rows of genes and columns representing samples. ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("flu.meta", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is a data frame, with rows of samples and columns of metadata information.", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure(list(structure("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30550", Rd_tag = "VERB")), Rd_tag = "\\url")), Rd_tag = "\\source"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Huang Y et al. (PLoS Genet 2011)\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/eset.full.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Huang Y et al. (PLoS Genet 2011)\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/eset.full.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ fluVaccine (list) = structure(list(structure(list(structure("Gene expression sets from Flu Vaccine trials", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fluVaccine", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fluVaccine", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ @@ -534,15 +534,15 @@ │ │ │ │ structure(list(structure(list(structure("fluVaccine", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is a list.", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59635", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59654", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Thakar J et al., Aging, 2015\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/fluVaccine.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Thakar J et al., Aging, 2015\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/fluVaccine.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getXcoords (list) = structure(list(structure(list(structure("Get the X coordinates for the points of the PDF", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getXcoords", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getXcoords", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Calculates the x-coordinates for the PDF of a given pathway.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -599,15 +599,15 @@ │ │ │ │ structure(" geneSets = list(diff.set=1:30, base.set=31:60)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##Run qusage\n", Rd_tag = "RCODE"), │ │ │ │ structure(" set.results = qusage(eset, labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##Plot the PDF (see also: plotDensityCurves() )\n", Rd_tag = "RCODE"), │ │ │ │ structure(" x = getXcoords(set.results, 1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" y = set.results$path.PDF[,1]\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plot(x,y, type=\"l\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/getXcoords.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/getXcoords.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ makeComparison (list) = structure(list(structure(list(structure("Compare Genes Between Two Groups", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("makeComparison", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("makeComparison", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -668,15 +668,15 @@ │ │ │ │ structure(" eset[1:30, labels==\"B\"] = eset[1:30, labels==\"B\"] + 1\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##compare the two groups\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results = makeComparison(eset, labels, \"B-A\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("## Paired Samples\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ##Group A and group B are two samples from the same set of 10 patients\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pairVector = c(1:10,1:10)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results.paired = makeComparison(eset, labels,\"B-A\",pairVector=pairVector)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/makeComparison.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/makeComparison.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ newQSarray (list) = structure(list(structure(list(structure("The qusage Array Object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("newQSarray", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("newQSarray", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" The constructor for the QSarray object. Should primarily be used internally by ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("qusage", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -708,15 +708,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("In order to create a QSarray object from scratch, the constructor requires the following three fields: ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("mean", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure("sd", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", and ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("dof", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(". All other fields can be either left blank or added after. Note that in some cases, various methods will not be able to run without more information. For a complete list of the fields that the QSarray object can contain, refer to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("QSarray-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/newQSarray.Rd", class = "Rd", meta = list( │ │ │ │ + structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/newQSarray.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ pVal (list) = structure(list(structure(list(structure("Calculate p-values for gene set activity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pVal", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pdf.pVal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("oneWay.pVal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("twoCurve.pVal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -807,15 +807,15 @@ │ │ │ │ structure(" A.results = qusage(eset,labels, \"A2-A1\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" B.results = qusage(eset,labels, \"B2-B1\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("##calculate p-values for initial comparison\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pdf.pVal(A.results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pdf.pVal(B.results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##compare the pdfs of the two groups\n", Rd_tag = "RCODE"), │ │ │ │ structure(" twoCurve.pVal(A.results,B.results)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/pVal.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/pVal.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotCIs (list) = structure(list(structure(list(structure("Plot Pathway Mean and Confidence Intervals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotCIs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotCIs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Functions for plotting the mean and confidence intervals of a set of pathways.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -953,15 +953,15 @@ │ │ │ │ structure(" eset[genes,labels==\"B\"] = eset[genes,labels==\"B\"] + rnorm(1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" geneSets[[paste(\"Set\",i)]] = genes\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##calculate qusage results\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results = qusage(eset,labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##Plot gene set CIs\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotCIs(results)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/plotCIs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCIs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotCIsGenes (list) = structure(list(structure(list(structure("Plot Gene Mean and Confidence Intervals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotCIsGenes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotCIsGenes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Functions for plotting the mean and confidence intervals of the genes in a pathway.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1080,15 +1080,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" geneSets = list(diffSet=diffSet, normSet=normSet)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("##calculate qusage results\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results = qusage(eset,labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##Plot gene data from first gene set\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotCIsGenes(results, path.index=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##Add a bar to represent the differential expression of the gene set\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotCIsGenes(results, path.index=1, pathwayCI=\"bar\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/plotCIsGenes.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCIsGenes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotCombinedPDF (list) = structure(list(structure(list(structure("Plot combined PDF for an individual pathway", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotCombinedPDF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotCombinedPDF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A function for plotting out the pdfs for an indivdiual pathway in the QScomb object.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1163,15 +1163,15 @@ │ │ │ │ structure(" set.results = lapply(esets, function(dat){\n", Rd_tag = "RCODE"), │ │ │ │ structure(" qusage(dat$eset, dat$labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" })\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure(" ##run the combinePDFs function\n", Rd_tag = "RCODE"), │ │ │ │ structure(" combined = combinePDFs(set.results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" ##plot the combined PDF result for \"diff.set\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotCombinedPDF(combined, path.index=\"diff.set\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/plotCombinedPDF.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" \n", Rd_tag = "RCODE"), structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotCombinedPDF.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotDensityCurves (list) = structure(list(structure(list(structure("Plot gene set PDFs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotDensityCurves", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotDensityCurves", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A function for plotting out the pdfs of a set of pathways.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1237,15 +1237,15 @@ │ │ │ │ structure(" coords = plotDensityCurves(set.results, plot=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plot(0, type=\"n\", xlim=c(-1,2),ylim=c(0,1),xlab=\"x\",ylab=\"CDF\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" for(i in 1:length(coords)){\n", Rd_tag = "RCODE"), │ │ │ │ structure(" points = coords[[i]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(" x = points$x\n", Rd_tag = "RCODE"), structure(" y = cumsum(points$y)/sum(points$y)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" lines(x,y,col=i)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/plotDensityCurves.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotDensityCurves.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotGeneSetDistributions (list) = structure(list(structure(list(structure("Plot gene and gene set PDFs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotGeneSetDistributions", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotGeneSetDistributions", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A function for plotting out the pdfs of all the genes in a gene set\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1369,15 +1369,15 @@ │ │ │ │ structure(" B.results = qusage(eset,labels, \"B2-B1\", geneSet)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("##plot the gene set distribution for group A and group B side-by-side\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotGeneSetDistributions(A.results,B.results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##add labels to the right side of the plots\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotGeneSetDistributions(A.results,B.results,groupLabel = c(\"A2-A1\", \"B2-B1\"), labelLoc=\"right\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##change the colors of the curves\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotGeneSetDistributions(A.results,B.results, colorScheme=\"rainbow\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/plotGeneSetDistributions.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/plotGeneSetDistributions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ qgen (list) = structure(list(structure(list(structure("Run qusage while incoprating generalized least squares and linear mixed model analysis at the gene level to account for repeated measures, continous covariates, and confounder adjusting.\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("qgen", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("qgen", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A wrapper function for the three primary steps in the qusage algorithm. The first step replaces the conventional t-test framework, with additional flexibility to incorporate general linear models from the nlme package, specifically the lme and gls function calls. \n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("qgen(eset,design,fixed,geneSets,\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1483,15 +1483,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("##Running a linear mixed model to test for D1 vs D0 for Condition B, with a subject\n", Rd_tag = "RCODE"), │ │ │ │ structure("## specific random effect\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("qs.result<-qgen(eset,des,geneSets=geneSets,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" fixed= ~Condition+Time+Time*Condition,random=~1|Donor,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" contrast.factor=~Condition*Time,contrast=\"BD1-BD0\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" design.sampleid=\"SampleID\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("plot(qs.result)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/qgen.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("plot(qs.result)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qgen.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ qsTable (list) = structure(list(structure(list(structure("Summary of QSarray Results", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("qsTable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("qsTable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Print a table with a summary of the information on the most significant gene sets in QSarray.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1542,15 +1542,15 @@ │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" geneSets[[paste(\"Set\",i)]] = genes\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##calculate qusage results\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results = qusage(eset,labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" qsTable(results)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##show the first 5 sets, sorted by log fold change\n", Rd_tag = "RCODE"), │ │ │ │ structure(" qsTable(results, number=5, sort.by=\"logFC\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/qsTable.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qsTable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ qusage (list) = structure(list(structure(list(structure("Run qusage on an expression dataset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("qusage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("qusage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A wrapper function for the three primary steps in the qusage algorithm\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1613,15 +1613,15 @@ │ │ │ │ structure(" for(i in 0:10){\n", Rd_tag = "RCODE"), structure(" genes = ((30*i)+1):(30*(i+1))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" eset[genes,labels==\"B\"] = eset[genes,labels==\"B\"] + rnorm(1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" geneSets[[paste(\"Set\",i)]] = genes\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure("##calculate qusage results\n", Rd_tag = "RCODE"), │ │ │ │ structure(" results = qusage(eset,labels, \"B-A\", geneSets)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" \n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/qusage.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/qusage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ read.gmt (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Read in gene set information from .gmt files\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("read.gmt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("read.gmt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads in and parses information from the MSigDB's .gmt files. Pathway information will be returned as a list of gene sets.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1631,15 +1631,15 @@ │ │ │ │ list(structure("The .gmt file to be read", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The .gmt format is a tab-delimited list of gene sets, where each line is a separate gene set. The first column must specify the name of the gene set, and the second column is used for a short description (which this function discards). For complete details on the .gmt format, refer to the Broad Institute's Data Format's page (url: ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure(").\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A list, where each index represents a separate gene set. \n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(list(structure("Warning", Rd_tag = "TEXT")), │ │ │ │ - list(structure("\n", Rd_tag = "TEXT"), structure(" The function does not check that the file is correctly formatted, and may return incorrect or partial gene sets, e.g. if the first two columns are omitted. Please make sure that files are correctly formatted before reading them in using this function.\n", Rd_tag = "TEXT"))), Rd_tag = "\\section")), Rdfile = "/home/moeller/Salsa/r-bioc-qusage/man/read.gmt.Rd", class = "Rd", meta = list( │ │ │ │ + list(structure("\n", Rd_tag = "TEXT"), structure(" The function does not check that the file is correctly formatted, and may return incorrect or partial gene sets, e.g. if the first two columns are omitted. Please make sure that files are correctly formatted before reading them in using this function.\n", Rd_tag = "TEXT"))), Rd_tag = "\\section")), Rdfile = "/build/reproducible-path/r-bioc-qusage-2.46.0/man/read.gmt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ ├── ./usr/lib/R/site-library/qusage/help/qusage.rdx │ │ │ ├── qusage.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,133 +1,133 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$GeneSets │ │ │ │ │ -[1] 276 1333 │ │ │ │ │ +[1] 282 1345 │ │ │ │ │ │ │ │ │ │ $variables$`QSarray-class` │ │ │ │ │ -[1] 1890 6266 │ │ │ │ │ +[1] 1911 6277 │ │ │ │ │ │ │ │ │ │ $variables$aggregateGeneSet │ │ │ │ │ -[1] 8439 3648 │ │ │ │ │ +[1] 8475 3658 │ │ │ │ │ │ │ │ │ │ $variables$calcBayesCI │ │ │ │ │ -[1] 12368 1632 │ │ │ │ │ +[1] 12419 1642 │ │ │ │ │ │ │ │ │ │ $variables$calcVIF │ │ │ │ │ -[1] 14278 4117 │ │ │ │ │ +[1] 14344 4126 │ │ │ │ │ │ │ │ │ │ $variables$combinePDFs │ │ │ │ │ -[1] 18676 2462 │ │ │ │ │ +[1] 18755 2473 │ │ │ │ │ │ │ │ │ │ $variables$eset.full │ │ │ │ │ -[1] 21418 2271 │ │ │ │ │ +[1] 21512 2281 │ │ │ │ │ │ │ │ │ │ $variables$fluVaccine │ │ │ │ │ -[1] 23969 1805 │ │ │ │ │ +[1] 24077 1815 │ │ │ │ │ │ │ │ │ │ $variables$getXcoords │ │ │ │ │ -[1] 26053 2902 │ │ │ │ │ +[1] 26176 2911 │ │ │ │ │ │ │ │ │ │ $variables$makeComparison │ │ │ │ │ -[1] 29238 3513 │ │ │ │ │ +[1] 29373 3525 │ │ │ │ │ │ │ │ │ │ $variables$newQSarray │ │ │ │ │ -[1] 33032 2042 │ │ │ │ │ +[1] 33183 2053 │ │ │ │ │ │ │ │ │ │ $variables$pVal │ │ │ │ │ -[1] 35349 4239 │ │ │ │ │ +[1] 35516 4248 │ │ │ │ │ │ │ │ │ │ $variables$plotCIs │ │ │ │ │ -[1] 39867 5378 │ │ │ │ │ +[1] 40047 5385 │ │ │ │ │ │ │ │ │ │ $variables$plotCIsGenes │ │ │ │ │ -[1] 45527 4724 │ │ │ │ │ +[1] 45717 4731 │ │ │ │ │ │ │ │ │ │ $variables$plotCombinedPDF │ │ │ │ │ -[1] 50535 3272 │ │ │ │ │ +[1] 50736 3280 │ │ │ │ │ │ │ │ │ │ $variables$plotDensityCurves │ │ │ │ │ -[1] 54094 3001 │ │ │ │ │ +[1] 54306 3009 │ │ │ │ │ │ │ │ │ │ $variables$plotGeneSetDistributions │ │ │ │ │ -[1] 57384 5171 │ │ │ │ │ +[1] 57606 5182 │ │ │ │ │ │ │ │ │ │ $variables$qgen │ │ │ │ │ -[1] 62830 5493 │ │ │ │ │ +[1] 63068 5502 │ │ │ │ │ │ │ │ │ │ $variables$qsTable │ │ │ │ │ -[1] 68602 2493 │ │ │ │ │ +[1] 68852 2501 │ │ │ │ │ │ │ │ │ │ $variables$qusage │ │ │ │ │ -[1] 71368 3632 │ │ │ │ │ +[1] 71632 3644 │ │ │ │ │ │ │ │ │ │ $variables$read.gmt │ │ │ │ │ -[1] 75279 1303 │ │ │ │ │ +[1] 75559 1317 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 276 │ │ │ │ │ +[1] 0 282 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 28955 283 │ │ │ │ │ +[1] 29087 286 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 32751 281 │ │ │ │ │ +[1] 32898 285 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 35074 275 │ │ │ │ │ +[1] 35236 280 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 39588 279 │ │ │ │ │ +[1] 39764 283 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 45245 282 │ │ │ │ │ +[1] 45432 285 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 50251 284 │ │ │ │ │ +[1] 50448 288 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 53807 287 │ │ │ │ │ +[1] 54016 290 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 57095 289 │ │ │ │ │ +[1] 57315 291 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 62555 275 │ │ │ │ │ +[1] 62788 280 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 68323 279 │ │ │ │ │ +[1] 68570 282 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1609 281 │ │ │ │ │ +[1] 1627 284 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 71095 273 │ │ │ │ │ +[1] 71353 279 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 75000 279 │ │ │ │ │ +[1] 75276 283 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 8156 283 │ │ │ │ │ +[1] 8188 287 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 12087 281 │ │ │ │ │ +[1] 12133 286 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 14000 278 │ │ │ │ │ +[1] 14061 283 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 18395 281 │ │ │ │ │ +[1] 18470 285 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 21138 280 │ │ │ │ │ +[1] 21228 284 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 23689 280 │ │ │ │ │ +[1] 23793 284 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 25774 279 │ │ │ │ │ +[1] 25892 284 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE