P53 dataset

P53 dataset

Usage

data(p53_dataset)

Format

An object of class list of length 4.

Details

P53 dataset as well as the C2 gene sets are from https://data.broadinstitute.org/gsea-msigdb/gsea/dataset_files/.

The following code is used to generate the dataset:

expr = read.table(url("https://data.broadinstitute.org/gsea-msigdb/gsea/dataset_files/P53_collapsed_symbols.gct"),
    skip = 2, header = TRUE, row.names = 1, sep = "\t", quote = "")
expr = as.matrix(expr[, -1])

condition = readLines(url("https://data.broadinstitute.org/gsea-msigdb/gsea/dataset_files/P53.cls"))[3]
condition = strsplit(condition, " ")[[1]]
condition = factor(condition, levels = c("MUT", "WT"))

ln = readLines(url("https://data.broadinstitute.org/gsea-msigdb/gsea/dataset_files/c2.symbols.gmt"))
lt = strsplit(ln, "\t")

gs = lapply(lt, function(x) x[-(1:2)])
names(gs) = sapply(lt, function(x) x[1])

library(matrixStats)
m1 = expr[, condition == "MUT"]
m2 = expr[, condition == "WT"]
s = (rowMeans(m1) - rowMeans(m2))/(rowSds(m1) + rowSds(m2))
s = sort(s, decreasing = TRUE)

p53_dataset = list(expr = expr, condition = condition, s2n = s, gs = gs)

A positive signal-to-noise ratio (s2n) means up-regulation in MUT.