mirror of
https://github.com/johrpan/ubigen.git
synced 2025-10-26 11:47:24 +01:00
33 lines
No EOL
632 B
R
33 lines
No EOL
632 B
R
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) |