counts: Gene expression data sample

In cTRAP: Identification of candidate causal perturbations from differential gene expression data

Description

Gene expression data sample obtained by running the following code:

data("ENCODEmetadata")
ENCODEsamples <- loadENCODEsamples(ENCODEmetadata)[[1]]
counts <- prepareENCODEgeneExpression(ENCODEsamples)

# Remove low coverage (at least 10 counts shared across two samples)
minReads   <- 10
minSamples <- 2
filter <- rowSums(counts[ , -c(1, 2)] >= minReads) >= minSamples
counts <- counts[filter, ]

# Convert ENSEMBL identifier to gene symbol
counts$gene_id <- convertENSEMBLtoGeneSymbols(counts$gene_id)

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.