data-raw/drug_annot/pug_view/get_cids.R

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

# get unique compound ids for 2-get_views.sh
setwd("~/Documents/Batcave/zaklab/dseqr/data-raw/drug_annot/pug_view")

cmap_pdata <- readRDS(system.file('extdata', 'CMAP02_pdata.rds', package = 'dseqr'))
l1000_pdata <- readRDS(system.file('extdata', 'L1000_pdata.rds', package = 'dseqr'))

cids <- c(cmap_pdata$`Pubchem CID`, l1000_pdata$`Pubchem CID`)
names(cids) <- c(cmap_pdata$title, l1000_pdata$title)
names(cids) <- gsub('^([^_]+)_.+?$', '\\1', names(cids))
cids <- cids[!duplicated(cids) & !is.na(cids) & cids != '-666']

write.table(cids, 'cids.csv', row.names = FALSE, col.names = FALSE, quote = FALSE)
saveRDS(cids, 'cids.rds')