pwOmics (version 1.4.0)

identifyRsofTFs: Identify regulators of enriched transcription factors - upstream analysis.

Description

This function identifies the regulators upstream of the enriched/identified transcription factors in upstream analysis. Converting the pathway information to a regulatory graph needs some time... Warnings regarding the skipping of edges in building the regulatory graph can be ignored.

Usage

identifyRsofTFs(data_omics, only_enriched = TRUE, noTFs_inPW = 2, order_neighbors = 6)

Arguments

data_omics

OmicsData object.

only_enriched

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

noTFs_inPW

integer; only regulators in upstream pathways with more than this number of TFs are identified.

order_neighbors

integer specifiying the order of the neighborhood: order 1 is TF plus its immediate neighbors.

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)
# setwd(system.file("extdata/Genelists", package = "pwOmics"))
# identifyRsofTFs(data_omics, only_enriched = FALSE, noTFs_inPW = 1,
# order_neighbors = 10)
# ## End(Not run)