counts: Gene expression data sample

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Gene expression data sample

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$gene_id <- convertGeneIdentifiers(counts$gene_id)

nuno-agostinho/cTRAP documentation built on Jan. 2, 2025, 12:11 a.m.