Load ENCODE gene expression data

Load ENCODE gene expression data

prepareENCODEgeneExpression(samples)

Arguments

samples

List of loaded ENCODE samples

Value

Data frame containing gene read counts

See also

convertGeneIdentifiers()

Other functions related with using ENCODE expression data: downloadENCODEknockdownMetadata(), loadENCODEsamples(), performDifferentialExpression()

Examples

if (interactive()) {
  # Load ENCODE metadata for a specific cell line and gene
  cellLine <- "HepG2"
  gene <- "EIF4G1"
  ENCODEmetadata <- downloadENCODEknockdownMetadata(cellLine, gene)

  # Load samples based on filtered ENCODE metadata
  ENCODEsamples <- loadENCODEsamples(ENCODEmetadata)[[1]]

  prepareENCODEgeneExpression(ENCODEsamples)
}