From 6a3ee45b353c22d64c556aa2250ae08aaf8d54a6 Mon Sep 17 00:00:00 2001 From: Alexey Sergushichev Date: Tue, 17 Oct 2023 13:38:18 -0500 Subject: [PATCH] Add description of inst/extdata/testdata files --- DESCRIPTION | 2 +- inst/script/testdata.md | 1 + vignettes/phantasusLite-tutorial.Rmd | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 inst/script/testdata.md diff --git a/DESCRIPTION b/DESCRIPTION index 5534cfa..c9381fa 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phantasusLite Type: Package Title: Loading and annotation RNA-Seq counts matrices -Version: 0.99.2 +Version: 0.99.3 Authors@R: c(person("Rita", "Sablina", role = "aut"), person("Maxim", "Kleverov", role = "aut"), person("Alexey", "Sergushichev", email = "alsergbox@gmail.com", role = c("aut", "cre"))) diff --git a/inst/script/testdata.md b/inst/script/testdata.md new file mode 100644 index 0000000..8b307e8 --- /dev/null +++ b/inst/script/testdata.md @@ -0,0 +1 @@ +`inst/extdata/testdata/gct` folder contains toy gene expression files in GCT format, generated for testing purposes. They are generated based on a small subset of GSE63040 and GSE53986 datasets. The initial versions of the files were obtained by exporting the corresponding datasets from Phantasus application. Additionally, files were manually modified to trigger certain code scenarios (e.g. by introducing duplicated IDs in `test_dup.gct`). diff --git a/vignettes/phantasusLite-tutorial.Rmd b/vignettes/phantasusLite-tutorial.Rmd index b18cc74..0943dd1 100755 --- a/vignettes/phantasusLite-tutorial.Rmd +++ b/vignettes/phantasusLite-tutorial.Rmd @@ -68,7 +68,7 @@ url <- 'https://ctlab.itmo.ru/hsds/?domain=/counts' getHSDSFileList(url) ``` -GSE53053 dataset was sequenced from Arabidopsis thaliana and we can get an expression matrix +GSE53053 dataset was sequenced from *Mus musculus* and we can get an expression matrix from the corresponding HDF5-file with DEE2 data: ```{r}