scripts: Add analysis of drug effects

scripts/cmap_drugs_input.R

@@ -0,0 +1,47 @@
+library(data.table)
+library(gprofiler2)
+library(here)
+
+i_am("scripts/cmap_drugs_input.R")
+
+# Source: custom
+load(here("scripts", "input", "CMap_20180808.RData"))
+
+data <- CMap$"HT_HG-U133A"
+rm(CMap)
+
+transcripts <- dimnames(data)$transcripts
+genes <- gconvert(
+  transcripts,
+  numeric_ns = "ENTREZGENE_ACC",
+  mthreshold = 1,
+  filter_na = FALSE
+)$target
+dimnames(data)[[1]] <- genes
+
+data_drugs <- as.data.table(data)
+data_drugs <- na.omit(data_drugs)
+data_drugs <- data_drugs[data == "logFoldChange", .(transcripts, drugs, value)]
+
+setnames(
+  data_drugs,
+  c("transcripts", "drugs", "value"),
+  c("gene", "drug", "change")
+)
+
+genes_0_0 <- scan(here("scripts/output/genes_0_0.txt"), what = character())
+genes_0_1 <- scan(here("scripts/output/genes_0_1.txt"), what = character())
+genes_1_0 <- scan(here("scripts/output/genes_1_0.txt"), what = character())
+genes_1_1 <- scan(here("scripts/output/genes_1_1.txt"), what = character())
+
+data_drugs[gene %chin% genes_0_0, group := "genes_0_0"]
+data_drugs[gene %chin% genes_0_1, group := "genes_0_1"]
+data_drugs[gene %chin% genes_1_0, group := "genes_1_0"]
+data_drugs[gene %chin% genes_1_1, group := "genes_1_1"]
+
+data_drugs <- na.omit(data_drugs)
+
+results <- data_drugs[, .(mean_change = mean(change)), by = .(drug, group)]
+fwrite(results, file = here("scripts/output/cmap_drugs.csv"))
+
+write(data_drugs[, unique(drug)], file = here("scripts/output/drugs.txt"))