pwOmics (version 1.4.0)

identifyPWTFTGs: Identify TFs in enriched pathways and their target genes - downstream analysis.

Description

This function identifies the transcription factors being part of the enriched pathways of downstream analysis. Subsequently it finds the target genes of these transcription factors from the selected TF-target gene database.

Usage

identifyPWTFTGs(data_omics, only_enriched = TRUE)

Arguments

data_omics

OmicsData object.

only_enriched

boolean value defining if transcription factors should be identified only for enriched pathways (TRUE); or for all identified pathways (FALSE); default is TRUE.

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 = FALSE)

## Not run: 
# data_omics = identifyPWs(data_omics_plus)
# data_omics = identifyTFs(data_omics)
# data_omics = enrichPWs(data_omics)
# identifyPWTFTGs(data_omics, only_enriched = FALSE)
# ## End(Not run)