pwOmics (version 1.4.0)

enrichTFs: Transcription factor enrichment - upstream analysis.

Description

This function does transcription factor enrichment for transcription factor identified to be upstream of the diff. expressed genes/transcripts in the omics data set imported with readOmics function. In order to use this function first read in the transcription factor target gene information via readTFdata and identify the upstream TFs of the differentially expressed genes/transcripts with the identifyTFs function.

Usage

enrichTFs(data_omics, method = "BH", alpha = 0.05, ...)

Arguments

data_omics

OmicsData object.

method

correction method for multiple testing correction as specified in p.adjust documentation; default is Benjamini & Hochberg correction.

alpha

significance level for transcription factor enrichment; default is alpha = 0.05.

...

further input parameters for multiple comparison adjustment.

Value

OmicsData object: list of 4 elements (OmicsD, PathwayD, TFtargetsD, Status); OmicsD containing omics data set + results (after analysis); PathwayD containing selected pathway databases + biopax model; TFtargetsD containing selected TF target gene databases + TF target gene data.

Examples

data(OmicsExampleData)
data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24),
tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
PWdatabase = c("biocarta"),
TFtargetdatabase = c("chea"))

setwd(system.file("extdata", package = "pwOmics"))
data_omics = readTFdata(data_omics)
data_omics_plus = readPWdata(data_omics,
loadgenelists = "Genelists")

## Not run: 
# data_omics = identifyPWs(data_omics_plus)
# data_omics = identifyTFs(data_omics)
# data_omics = enrichTFs(data_omics)
# ## End(Not run)