--- /srv/rebuilderd/tmp/rebuilderdhAGGwI/inputs/r-bioc-qtlizer_1.26.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdhAGGwI/out/r-bioc-qtlizer_1.26.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-07 10:43:17.000000 debian-binary │ --rw-r--r-- 0 0 0 1576 2026-08-07 10:43:17.000000 control.tar.xz │ --rw-r--r-- 0 0 0 27380 2026-08-07 10:43:17.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1568 2026-08-07 10:43:17.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 27424 2026-08-07 10:43:17.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 785 2026-08-07 10:43:17.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 768 2026-08-07 10:43:17.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 2364 2026-08-07 10:43:17.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-qtlizer │ │ │ Version: 1.26.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ Installed-Size: 86 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-httr, r-cran-curl, r-bioc-genomicranges, r-cran-stringi, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocstyle, r-cran-testthat, r-cran-knitr, r-cran-rmarkdown │ │ │ +Suggests: r-bioc-biocstyle, r-cran-knitr, r-cran-rmarkdown │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/Qtlizer/ │ │ │ Description: Comprehensive QTL annotation of GWAS results │ │ │ This R package provides access to the Qtlizer web server. Qtlizer │ │ │ annotates lists of common small variants (mainly SNPs) and genes in │ │ │ humans with associated changes in gene expression using the most │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -15,29 +15,29 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 203 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1281 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 194 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 63 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 887 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/Qtlizer │ │ │ --rw-r--r-- 0 root (0) root (0) 8493 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 311 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 8505 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 314 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 4548 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1601 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.R │ │ │ -rw-r--r-- 0 root (0) root (0) 3080 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 9966 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.html │ │ │ --rw-r--r-- 0 root (0) root (0) 4656 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.md │ │ │ +-rw-r--r-- 0 root (0) root (0) 9770 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 4477 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.md │ │ │ -rw-r--r-- 0 root (0) root (0) 1638 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 68 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 4765 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 217 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 4848 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 222 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 110 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 160 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 175 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1270 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-07 10:43:17.000000 ./usr/lib/R/site-library/Qtlizer/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 10:43:17.000000 ./usr/share/doc/r-bioc-qtlizer/ │ │ │ -rw-r--r-- 0 root (0) root (0) 835 2026-08-07 10:43:17.000000 ./usr/share/doc/r-bioc-qtlizer/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -1,15 +1,15 @@ │ │ │ │ .__NAMESPACE__. (environment) = │ │ │ │ { │ │ │ │ "S3methods" = "structure(character(0), dim = c(0L, 4L))" │ │ │ │ "dynlibs" = "NULL" │ │ │ │ "exports" = "" │ │ │ │ "imports" = "list(base = TRUE)" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-qtlizer/debian/r-bioc-qtlizer/usr/lib/R/site-library/Qtlizer"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/debian/r-bioc-qtlizer/usr/lib/R/site-library/Qtlizer"" │ │ │ │ "spec" = "c(name = "Qtlizer", version = "1.26.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/Qtlizer/R/Qtlizer.rdx │ │ │ ├── Qtlizer.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,40 +1,40 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 597 52 │ │ │ │ │ +[1] 609 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 780 52 │ │ │ │ │ +[1] 792 52 │ │ │ │ │ │ │ │ │ │ $variables$.onLoad │ │ │ │ │ -[1] 832 610 │ │ │ │ │ +[1] 844 610 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 1442 52 │ │ │ │ │ +[1] 1454 52 │ │ │ │ │ │ │ │ │ │ $variables$communicate │ │ │ │ │ -[1] 1494 2581 │ │ │ │ │ +[1] 1506 2581 │ │ │ │ │ │ │ │ │ │ $variables$get_qtls │ │ │ │ │ -[1] 4075 3653 │ │ │ │ │ +[1] 4087 3653 │ │ │ │ │ │ │ │ │ │ $variables$vector_split │ │ │ │ │ -[1] 7728 765 │ │ │ │ │ +[1] 7740 765 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 289 308 │ │ │ │ │ +[1] 289 320 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 158 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 649 131 │ │ │ │ │ +[1] 661 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.html │ │ │ @@ -103,15 +103,15 @@ │ │ │ body { max-width: 100%; } │ │ │ tr, img { break-inside: avoid; } │ │ │ } │ │ │ @media only screen and (min-width: 992px) { │ │ │ body:not(.pagesjs) pre:has(.line-numbers):not(:hover) { white-space: pre; } │ │ │ } │ │ │ │ │ │ - │ │ │ + │ │ │ │ │ │ │ │ │
│ │ │

Qtlizer: comprehensive QTL annotation of GWAS results

│ │ │

Julia Remes & Matthias Munz

│ │ │
│ │ │
│ │ │ @@ -121,92 +121,89 @@ │ │ │ 
if(!requireNamespace("BiocManager", quietly = TRUE))
│ │ │      install.packages("BiocManager")
│ │ │  BiocManager::install("Qtlizer")
│ │ │
│ │ │

Loading package

│ │ │ 
library(Qtlizer)
│ │ │  #> Error in `library()`:
│ │ │ -#> ! es gibt kein Paket namens 'Qtlizer'
│ │ │ +#> ! there is no package called 'Qtlizer'
│ │ │
│ │ │

Example function calls

│ │ │

The Qtlizer database can be queried with the function get_qtls. Accepted query terms are variant and gene identifiers of the form

│ │ │
    │ │ │
  • Rsid : rs + number e.g. “rs4284742”
    • │ │ │
  • reference:chr:pos e.g. “hg19:19:45412079” (Allowed references: hg19/GRCh37, hg38/GRCh38; accepted chromosomes are 1-22)
    • │ │ │
  • Gene symbol consisting of letters and numbers according to https://www.genenames.org/about/guidelines/
    • │ │ │
│ │ │ 
# Call get_qtls with a variant as a single query term
│ │ │  get_qtls("rs4284742")
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │
│ │ │

Common seperators (space, comma, space + comma, …) are accepted. Multiple terms can be passed in a single string, each term separated by comma, whitespace or both:

│ │ │ 
# Call get_qtls with multiple query terms in single string
│ │ │  df = get_qtls("rs4284742, rs2070901")
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │
│ │ │

Alternatively, terms can be passed as a vector:

│ │ │ 
# Call get_qtls with multiple query terms as vector
│ │ │  df = get_qtls(c("rs4284742", "DEFA1"))
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │
│ │ │

Input variants can be enriched by variants in linkage disequilibrium (LD). The correlation method to be used can be set with ld_method. Default is “r2”, alternatively “dprime” can be used. The correlation threshold, above which other correlated variants should be included, can be set with corr and ranges between 0 and 1. Default is “NA”

│ │ │ 
# Use parameters corr and ld_method
│ │ │  df = get_qtls(c("rs4284742", "DEFA1"), corr = 0.8, ld_method = "r2")
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │
│ │ │

Also, column descriptions can be viewed:

│ │ │ 
# View meta info
│ │ │  df = get_qtls("rs4284742")
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │  comment(df)
│ │ │  #> NULL
│ │ │
│ │ │

The QTL results is returned as data frame by default or as GenomicRanges::GRanges object. To return the results as GenomicRanges::GRanges object, return_obj is set to “granges”. If return_obj is set to “granges”, parameter ref_version sets the reference version in which the GRange object is returned. Allowed values are “hg19” (GRCh37) by default and “hg38” (GRCh38).

│ │ │ 
# Return result as GRange object with ref_version hg38
│ │ │  granges = get_qtls("rs4284742", return_obj = "granges", ref_version = "hg38")
│ │ │  #> Error in `get_qtls()`:
│ │ │ -#> ! konnte Funktion "get_qtls" nicht finden
│ │ │ +#> ! could not find function "get_qtls"
│ │ │
│ │ │

Output of Session Info

│ │ │

The output of sessionInfo() on the system │ │ │ on which this document was compiled:

│ │ │ 
sessionInfo()
│ │ │  #> R version 4.6.1 (2026-06-24)
│ │ │  #> Platform: x86_64-pc-linux-gnu
│ │ │  #> Running under: Debian GNU/Linux forky/sid
│ │ │  #> 
│ │ │  #> Matrix products: default
│ │ │  #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
│ │ │  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.30.so;  LAPACK version 3.12.0
│ │ │  #> 
│ │ │  #> locale:
│ │ │ -#>  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
│ │ │ -#>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
│ │ │ -#>  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
│ │ │ -#>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
│ │ │ -#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
│ │ │ -#> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
│ │ │ +#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
│ │ │ +#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
│ │ │ +#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
│ │ │ +#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
│ │ │  #> 
│ │ │ -#> time zone: Europe/Berlin
│ │ │ +#> time zone: Etc/UTC
│ │ │  #> tzcode source: system (glibc)
│ │ │  #> 
│ │ │  #> attached base packages:
│ │ │  #> [1] stats     graphics  grDevices utils     datasets  methods   base     
│ │ │  #> 
│ │ │  #> other attached packages:
│ │ │  #> [1] markdown_2.0 knitr_1.51  
│ │ │  #> 
│ │ │  #> loaded via a namespace (and not attached):
│ │ │ -#>  [1] compiler_4.6.1  cli_3.6.6       tools_4.6.1     pillar_1.11.1  
│ │ │ -#>  [5] otel_0.2.0      glue_1.8.1      vctrs_0.7.3     xfun_0.58      
│ │ │ -#>  [9] lifecycle_1.0.5 rlang_1.3.0     evaluate_1.0.5
│ │ │ +#> [1] compiler_4.6.1 cli_3.6.6      tools_4.6.1    otel_0.2.0     xfun_0.58     
│ │ │ +#> [6] rlang_1.3.0    evaluate_1.0.5
│ │ │
│ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -8,90 +8,88 @@ │ │ │ │ ************ IInnssttaallllaattiioonn ************ │ │ │ │ if(!requireNamespace("BiocManager", quietly = TRUE)) │ │ │ │ install.packages("BiocManager") │ │ │ │ BiocManager::install("Qtlizer") │ │ │ │ ************ LLooaaddiinngg ppaacckkaaggee ************ │ │ │ │ library(Qtlizer) │ │ │ │ #> Error in `library()`: │ │ │ │ -#> ! es gibt kein Paket namens 'Qtlizer' │ │ │ │ +#> ! there is no package called 'Qtlizer' │ │ │ │ ************ EExxaammppllee ffuunnccttiioonn ccaallllss ************ │ │ │ │ The Qtlizer database can be queried with the function get_qtls. Accepted query │ │ │ │ terms are variant and gene identifiers of the form │ │ │ │ * Rsid : rs + number e.g. “rs4284742” │ │ │ │ * reference:chr:pos e.g. “hg19:19:45412079” (Allowed references: hg19/ │ │ │ │ GRCh37, hg38/GRCh38; accepted chromosomes are 1-22) │ │ │ │ * Gene symbol consisting of letters and numbers according to _h_t_t_p_s_:_/_/ │ │ │ │ _w_w_w_._g_e_n_e_n_a_m_e_s_._o_r_g_/_a_b_o_u_t_/_g_u_i_d_e_l_i_n_e_s_/ │ │ │ │ # Call get_qtls with a variant as a single query term │ │ │ │ get_qtls("rs4284742") │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ Common seperators (space, comma, space + comma, …) are accepted. Multiple terms │ │ │ │ can be passed in a single string, each term separated by comma, whitespace or │ │ │ │ both: │ │ │ │ # Call get_qtls with multiple query terms in single string │ │ │ │ df = get_qtls("rs4284742, rs2070901") │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ Alternatively, terms can be passed as a vector: │ │ │ │ # Call get_qtls with multiple query terms as vector │ │ │ │ df = get_qtls(c("rs4284742", "DEFA1")) │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ Input variants can be enriched by variants in linkage disequilibrium (LD). The │ │ │ │ correlation method to be used can be set with ld_method. Default is “r2”, │ │ │ │ alternatively “dprime” can be used. The correlation threshold, above which │ │ │ │ other correlated variants should be included, can be set with corr and ranges │ │ │ │ between 0 and 1. Default is “NA” │ │ │ │ # Use parameters corr and ld_method │ │ │ │ df = get_qtls(c("rs4284742", "DEFA1"), corr = 0.8, ld_method = "r2") │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ Also, column descriptions can be viewed: │ │ │ │ # View meta info │ │ │ │ df = get_qtls("rs4284742") │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ comment(df) │ │ │ │ #> NULL │ │ │ │ The QTL results is returned as data frame by default or as GenomicRanges:: │ │ │ │ GRanges object. To return the results as GenomicRanges::GRanges object, │ │ │ │ return_obj is set to “granges”. If return_obj is set to “granges”, parameter │ │ │ │ ref_version sets the reference version in which the GRange object is returned. │ │ │ │ Allowed values are “hg19” (GRCh37) by default and “hg38” (GRCh38). │ │ │ │ # Return result as GRange object with ref_version hg38 │ │ │ │ granges = get_qtls("rs4284742", return_obj = "granges", ref_version = "hg38") │ │ │ │ #> Error in `get_qtls()`: │ │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ │ +#> ! could not find function "get_qtls" │ │ │ │ ************ OOuuttppuutt ooff SSeessssiioonn IInnffoo ************ │ │ │ │ The output of sessionInfo() on the system on which this document was compiled: │ │ │ │ sessionInfo() │ │ │ │ #> R version 4.6.1 (2026-06-24) │ │ │ │ #> Platform: x86_64-pc-linux-gnu │ │ │ │ #> Running under: Debian GNU/Linux forky/sid │ │ │ │ #> │ │ │ │ #> Matrix products: default │ │ │ │ #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 │ │ │ │ #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.30.so; │ │ │ │ LAPACK version 3.12.0 │ │ │ │ #> │ │ │ │ #> locale: │ │ │ │ -#> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C │ │ │ │ -#> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 │ │ │ │ -#> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 │ │ │ │ -#> [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C │ │ │ │ -#> [9] LC_ADDRESS=C LC_TELEPHONE=C │ │ │ │ -#> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C │ │ │ │ +#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 │ │ │ │ +#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 │ │ │ │ +#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C │ │ │ │ +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C │ │ │ │ #> │ │ │ │ -#> time zone: Europe/Berlin │ │ │ │ +#> time zone: Etc/UTC │ │ │ │ #> tzcode source: system (glibc) │ │ │ │ #> │ │ │ │ #> attached base packages: │ │ │ │ #> [1] stats graphics grDevices utils datasets methods base │ │ │ │ #> │ │ │ │ #> other attached packages: │ │ │ │ #> [1] markdown_2.0 knitr_1.51 │ │ │ │ #> │ │ │ │ #> loaded via a namespace (and not attached): │ │ │ │ -#> [1] compiler_4.6.1 cli_3.6.6 tools_4.6.1 pillar_1.11.1 │ │ │ │ -#> [5] otel_0.2.0 glue_1.8.1 vctrs_0.7.3 xfun_0.58 │ │ │ │ -#> [9] lifecycle_1.0.5 rlang_1.3.0 evaluate_1.0.5 │ │ │ │ +#> [1] compiler_4.6.1 cli_3.6.6 tools_4.6.1 otel_0.2.0 xfun_0.58 │ │ │ │ + │ │ │ │ +#> [6] rlang_1.3.0 evaluate_1.0.5 │ │ ├── ./usr/lib/R/site-library/Qtlizer/doc/Qtlizer.md │ │ │ @@ -24,77 +24,77 @@ │ │ │ ``` │ │ │ │ │ │ # Loading package │ │ │ │ │ │ ``` r │ │ │ library(Qtlizer) │ │ │ #> Error in `library()`: │ │ │ -#> ! es gibt kein Paket namens 'Qtlizer' │ │ │ +#> ! there is no package called 'Qtlizer' │ │ │ ``` │ │ │ │ │ │ # Example function calls │ │ │ The Qtlizer database can be queried with the function `get_qtls`. Accepted query terms are variant and gene identifiers of the form │ │ │ │ │ │ + Rsid : rs + number e.g. "rs4284742" │ │ │ + reference:chr:pos e.g. "hg19:19:45412079" (Allowed references: hg19/GRCh37, hg38/GRCh38; accepted chromosomes are 1-22) │ │ │ + Gene symbol consisting of letters and numbers according to [https://www.genenames.org/about/guidelines/]( https://www.genenames.org/about/guidelines/) │ │ │ │ │ │ │ │ │ ``` r │ │ │ # Call get_qtls with a variant as a single query term │ │ │ get_qtls("rs4284742") │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ ``` │ │ │ │ │ │ Common seperators (space, comma, space + comma, ...) are accepted. Multiple terms can be passed in a single string, each term separated by comma, whitespace or both: │ │ │ │ │ │ ``` r │ │ │ # Call get_qtls with multiple query terms in single string │ │ │ df = get_qtls("rs4284742, rs2070901") │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ ``` │ │ │ │ │ │ Alternatively, terms can be passed as a vector: │ │ │ │ │ │ ``` r │ │ │ # Call get_qtls with multiple query terms as vector │ │ │ df = get_qtls(c("rs4284742", "DEFA1")) │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ ``` │ │ │ │ │ │ Input variants can be enriched by variants in linkage disequilibrium (LD). The correlation method to be used can be set with `ld_method`. Default is "r2", alternatively "dprime" can be used. The correlation threshold, above which other correlated variants should be included, can be set with `corr` and ranges between 0 and 1. Default is "NA" │ │ │ │ │ │ ``` r │ │ │ # Use parameters corr and ld_method │ │ │ df = get_qtls(c("rs4284742", "DEFA1"), corr = 0.8, ld_method = "r2") │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ ``` │ │ │ │ │ │ Also, column descriptions can be viewed: │ │ │ │ │ │ ``` r │ │ │ # View meta info │ │ │ df = get_qtls("rs4284742") │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ comment(df) │ │ │ #> NULL │ │ │ ``` │ │ │ │ │ │ The QTL results is returned as data frame by default or as `GenomicRanges::GRanges` object. To return the results as GenomicRanges::GRanges object, `return_obj` is set to "granges". If `return_obj` is set to "granges", parameter `ref_version` sets the reference version in which the GRange object is returned. Allowed values are "hg19" (GRCh37) by default and "hg38" (GRCh38). │ │ │ │ │ │ ``` r │ │ │ # Return result as GRange object with ref_version hg38 │ │ │ granges = get_qtls("rs4284742", return_obj = "granges", ref_version = "hg38") │ │ │ #> Error in `get_qtls()`: │ │ │ -#> ! konnte Funktion "get_qtls" nicht finden │ │ │ +#> ! could not find function "get_qtls" │ │ │ ``` │ │ │ │ │ │ # Output of Session Info │ │ │ The output of ```sessionInfo()``` on the system │ │ │ on which this document was compiled: │ │ │ │ │ │ ``` r │ │ │ @@ -104,29 +104,26 @@ │ │ │ #> Running under: Debian GNU/Linux forky/sid │ │ │ #> │ │ │ #> Matrix products: default │ │ │ #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 │ │ │ #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.30.so; LAPACK version 3.12.0 │ │ │ #> │ │ │ #> locale: │ │ │ -#> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C │ │ │ -#> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 │ │ │ -#> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 │ │ │ -#> [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C │ │ │ -#> [9] LC_ADDRESS=C LC_TELEPHONE=C │ │ │ -#> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C │ │ │ +#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 │ │ │ +#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 │ │ │ +#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C │ │ │ +#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C │ │ │ #> │ │ │ -#> time zone: Europe/Berlin │ │ │ +#> time zone: Etc/UTC │ │ │ #> tzcode source: system (glibc) │ │ │ #> │ │ │ #> attached base packages: │ │ │ #> [1] stats graphics grDevices utils datasets methods base │ │ │ #> │ │ │ #> other attached packages: │ │ │ #> [1] markdown_2.0 knitr_1.51 │ │ │ #> │ │ │ #> loaded via a namespace (and not attached): │ │ │ -#> [1] compiler_4.6.1 cli_3.6.6 tools_4.6.1 pillar_1.11.1 │ │ │ -#> [5] otel_0.2.0 glue_1.8.1 vctrs_0.7.3 xfun_0.58 │ │ │ -#> [9] lifecycle_1.0.5 rlang_1.3.0 evaluate_1.0.5 │ │ │ +#> [1] compiler_4.6.1 cli_3.6.6 tools_4.6.1 otel_0.2.0 xfun_0.58 │ │ │ +#> [6] rlang_1.3.0 evaluate_1.0.5 │ │ │ ``` │ │ ├── ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ list(structure("Linkage disequilibrium based on 1000 Genomes Phase 3 European.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Optional value between 0 and 1. Default value is NA.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("ld_method", Rd_tag = "TEXT")), │ │ │ │ list(structure("There are two methods. Default method is \"r2\". \n", Rd_tag = "TEXT"), │ │ │ │ structure("The other opportunity is to use \"dprime\".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Data frame with results.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-qtlizer/man/communicate.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Data frame with results.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/communicate.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_qtls (list) = structure(list(structure(list(structure("Query Qtlizer", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_qtls", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_qtls", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Query Qtlizer database for expression quantitative \n", Rd_tag = "TEXT"), │ │ │ │ structure("trait loci (eQTLs) in human.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -54,15 +54,15 @@ │ │ │ │ structure("as data frame or as a GenomicRanges::GRanges object. The default value is \"dataframe\".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Data frame or GenomicRanges::GRanges object containing QTL data.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("get_qtls(\"rs4284742\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("get_qtls(c(\"rs4284742\", \"DEFA1\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("get_qtls(\"rs4284742,DEFA1\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("get_qtls(\"rs4284742\", return_obj=\"granges\", ref_version=\"hg38\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_qtls(\"rs4284742\", corr=0.6)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-qtlizer/man/get_qtls.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_qtls(\"rs4284742\", corr=0.6)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/get_qtls.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ @@ -80,10 +80,10 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vector_split(v, n)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("v", Rd_tag = "TEXT")), list(structure("input vector", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("n", Rd_tag = "TEXT")), │ │ │ │ list(structure("number of subvectors", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("List with subvectors.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-qtlizer/man/vector_split.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("List with subvectors.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/vector_split.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/Qtlizer/help/Qtlizer.rdx │ │ │ ├── Qtlizer.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,25 +1,25 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$communicate │ │ │ │ │ -[1] 280 1104 │ │ │ │ │ +[1] 293 1116 │ │ │ │ │ │ │ │ │ │ $variables$get_qtls │ │ │ │ │ -[1] 1664 2019 │ │ │ │ │ +[1] 1701 2038 │ │ │ │ │ │ │ │ │ │ $variables$vector_split │ │ │ │ │ -[1] 3966 799 │ │ │ │ │ +[1] 4033 815 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 280 │ │ │ │ │ +[1] 0 293 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1384 280 │ │ │ │ │ +[1] 1409 292 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 3683 283 │ │ │ │ │ +[1] 3739 294 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/Qtlizer/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,5 +1,5 @@ │ │ │ │ │ -[1] "/home/moeller/Salsa/r-bioc-qtlizer/man/communicate.Rd" │ │ │ │ │ -[2] "/home/moeller/Salsa/r-bioc-qtlizer/man/get_qtls.Rd" │ │ │ │ │ -[3] "/home/moeller/Salsa/r-bioc-qtlizer/man/vector_split.Rd" │ │ │ │ │ +[1] "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/communicate.Rd" │ │ │ │ │ +[2] "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/get_qtls.Rd" │ │ │ │ │ +[3] "/build/reproducible-path/r-bioc-qtlizer-1.26.0+dfsg/man/vector_split.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 40 │ │ │ │ │ +[1] 57