counts {cTRAP}R Documentation

Gene expression data sample

Description

Gene expression data sample obtained by running the following code:

gene <- "EIF4G1"
cellLine <- "HepG2"

ENCODEmetadata <- downloadENCODEknockdownMetadata(cellLine, gene)
table(ENCODEmetadata$`Experiment target`)
length(unique(ENCODEmetadata$`Experiment target`))

ENCODEsamples <- downloadENCODEsamples(ENCODEmetadata)
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, ]

[Package cTRAP version 1.2.0 Index]