Added CTRP treatmentIDs to use for examples and test suite

R/data.R

@@ -45,4 +45,22 @@
 #' data(cell_model_passports_models)
 #' head(cell_model_passports_models)
 #' @source https://cog.sanger.ac.uk/cmp/download/model_list_20240103.csv
-"cell_model_passports_models"
+"cell_model_passports_models"
+
+
+#' ctrp_treatmentIDs is a preprocessed version of the CTRP treatment metadata. 
+#' 
+#' Data was obtained from "https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/CTRPv2.0_2015_ctd2_ExpandedDataset.zip"
+#' and preprocessed to only get two columns: CTRP.treatmentid and CTRP.broad_cpd_id.
+#' 
+#' @format A data table with 2 columns and 545 rows.
+#' \describe{
+#' \item{CTRP.treatmentid}{`char` The treatment id of the all the compounds used in the experiment.}
+#' \item{CTRP.broad_cpd_id}{`char` The broad compound id of the all the compounds used in the experiment.}
+#' }
+#' @usage data(ctrp_treatmentIDs)
+#' @examples
+#' data(ctrp_treatmentIDs)
+#' head(ctrp_treatmentIDs)
+#' @source https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/CTRPv2.0_2015_ctd2_ExpandedDataset.zip
+"ctrp_treatmentIDs"

data-raw/ctrp_treatmentMetadata.R

@@ -0,0 +1,14 @@
+## File: v20.meta.per_compound.txt
+## obtained from "https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/CTRPv2.0_2015_ctd2_ExpandedDataset.zip"
+
+# Load the treatment metadata file
+filePath <- system.file("extdata", "v20.meta.per_compound.txt", package = "AnnotationGx")
+ctrp_treatmentIDs <- data.table::fread(filePath)[, .(cpd_name, broad_cpd_id)]
+
+# Rename the columns
+data.table::setnames(
+    ctrp_treatmentIDs, 
+    c("cpd_name", "broad_cpd_id"), c("CTRP.treatmentid", "CTRP.broad_cpd_id"))
+
+# Save the treatment metadata as a data object
+usethis::use_data(ctrp_treatmentIDs, overwrite = TRUE)