refactor: gzip data files

CCBR · Oct 8, 2024 · 9f8fae6 · 9f8fae6
1 parent 7af5758
commit 9f8fae6
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Showing 19 changed files with 17 additions and 110,187 deletions.
diff --git a/R/0_renee-class.R b/R/0_renee-class.R
@@ -42,11 +42,11 @@ reneeDataSet <- S7::new_class("renee",
 #' @examples
 #' renee_ds <- create_reneeDataSet_from_files(
 #'   sample_meta_filepath = system.file("extdata",
-#'     "sample_metadata.tsv",
+#'     "sample_metadata.tsv.gz",
 #'     package = "reneeTools"
 #'   ),
 #'   gene_counts_filepath = system.file("extdata",
-#'     "RSEM.genes.expected_count.all_samples.txt",
+#'     "RSEM.genes.expected_count.all_samples.txt.gz",
 #'     package = "reneeTools"
 #'   )
 #' )

diff --git a/R/deseq2.R b/R/deseq2.R
@@ -10,11 +10,11 @@
 #' @examples
 #' \dontrun{
 #' renee_ds <- create_reneeDataSet_from_files(
-#'   system.file("extdata", "sample_metadata.tsv",
+#'   system.file("extdata", "sample_metadata.tsv.gz",
 #'     package = "reneeTools"
 #'   ),
 #'   system.file("extdata",
-#'     "RSEM.genes.expected_count.all_samples.txt",
+#'     "RSEM.genes.expected_count.all_samples.txt.gz",
 #'     package = "reneeTools"
 #'   )
 #' ) %>% filter_counts()

diff --git a/R/metadata.R b/R/metadata.R
@@ -9,7 +9,7 @@
 #'
 #' @examples
 #' sample_meta_tbl <- readr::read_tsv(system.file("extdata",
-#'   "sample_metadata.tsv",
+#'   "sample_metadata.tsv.gz",
 #'   package = "reneeTools"
 #' ))
 #' head(sample_meta_tbl)

diff --git a/data-raw/gene_counts.R b/data-raw/gene_counts.R
@@ -1,3 +1,3 @@
 # WT_S1.RSEM.genes.results was generated from running RENEE v2.5.3 on the test dataset https://github.com/CCBR/RENEE/tree/e08f7db6c6e638cfd330caa182f64665d2ef37fa/.tests
-gene_counts <- readr::read_tsv(system.file("inst", "extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"))
+gene_counts <- readr::read_tsv(system.file("inst", "extdata", "RSEM.genes.expected_count.all_samples.txt.gz", package = "reneeTools"))
 usethis::use_data(gene_counts, overwrite = TRUE)
diff --git a/data-raw/nidap.R b/data-raw/nidap.R
@@ -1,21 +1,21 @@
 ## training data set from the NIDAP Bulk RNA-seq workflow
 
 nidap_clean_raw_counts <- readr::read_csv(system.file(
-  "extdata", "nidap", "Clean_Raw_Counts.csv",
+  "extdata", "nidap", "Clean_Raw_Counts.csv.gz",
   package = "reneeTools"
 ))
 usethis::use_data(nidap_clean_raw_counts, overwrite = TRUE)
 
 nidap_sample_metadata <- readr::read_csv(system.file(
   "extdata", "nidap",
-  "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv",
+  "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz",
   package = "reneeTools"
 ))
 usethis::use_data(nidap_sample_metadata, overwrite = TRUE)
 
 nidap_filtered_counts <- readr::read_csv(system.file(
   "extdata", "nidap",
-  "Filtered_Counts.csv",
+  "Filtered_Counts.csv.gz",
   package = "reneeTools"
 ))
 usethis::use_data(nidap_filtered_counts, overwrite = TRUE)