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 1.0.3 Index]