pwOmics (version 1.4.0)

identifyTFs: Transcription factor identification.

Description

This function identifies the upstream transcription factors of the provided gene IDs.

Usage

identifyTFs(data_omics)

Arguments

data_omics

OmicsData object.

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"))

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)
# ## End(Not run)