performDifferentialExpression: Perform differential gene expression based on ENCODE data

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

Description

Perform differential gene expression based on ENCODE data

Usage

performDifferentialExpression(counts)

Arguments

counts

Data frame: gene expression

Value

Data frame with differential gene expression results between knockdown and control

See Also

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

Examples

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

  # Download samples based on filtered ENCODE metadata
  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$gene_id <- convertENSEMBLtoGeneSymbols(counts$gene_id)

  # Perform differential gene expression analysis
  diffExpr <- performDifferentialExpression(counts)
}

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