loadENCODEsamples: Load ENCODE samples

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Load ENCODE samples

Description

Samples are automatically downloaded if they are not found in the current working directory.

Usage

loadENCODEsamples(metadata, path = ".")

Arguments

metadata	Character: ENCODE metadata
path	Character: path where to download files

Value

List of loaded ENCODE samples

See Also

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

Examples

if (interactive()) {
  # Load ENCODE metadata for a specific cell line and gene
  cellLine <- "HepG2"
  gene <- c("EIF4G1", "U2AF2")
  ENCODEmetadata <- downloadENCODEknockdownMetadata(cellLine, gene)

  # Load samples based on filtered ENCODE metadata
  loadENCODEsamples(ENCODEmetadata)
}

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.