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