Add CMap dataset

scripts/cmap.R

@@ -0,0 +1,33 @@
+library(data.table)
+library(gprofiler2)
+library(here)
+
+i_am("scripts/cmap.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
+
+d <- as.data.table(data)
+d <- na.omit(d)
+d <- d[data == "logMean", .(transcripts, drugs, value)]
+
+setnames(
+  d,
+  c("transcripts", "drugs", "value"),
+  c("gene", "sample", "expression")
+)
+
+cmap <- ubigen::analyze(d)
+usethis::use_data(cmap, overwrite = TRUE)