prepareENCODEgeneExpression: Load ENCODE gene expression data

In cTRAP: Identification of candidate causal perturbations from differential gene expression data

Description

Load ENCODE gene expression data

Usage

prepareENCODEgeneExpression(samples)

Arguments

samples

List of loaded ENCODE samples

Value

Data frame containing gene read counts

See Also

convertENSEMBLtoGeneSymbols()

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)
}

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.