counts {cTRAP} | R Documentation

## 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)

[Package cTRAP version 1.12.0 Index]