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