pwOmics (version 1.4.0)

getDS_TFs: Get downstream analysis transcription factors in pathways.

Description

This function returns the genes identified in the downstream analysis and a column indicating if the genes are transcription factors.

Usage

getDS_TFs(data_omics)

Arguments

data_omics
OmicsData object.

Value

list of length = number of protein time points, each element containing a character vector with identified transcription factors.

Examples

Run this code
#please run with whole database files (prepared according to vignette)
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", "kegg", "nci", "reactome"),
TFtargetdatabase = c("chea", "pazar"))
## Not run: 
# data_omics = readTFdata(data_omics)
# data_omics_plus = readPWdata(data_omics,
# loadgenelists = FALSE)
# data_omics = identifyPWs(data_omics_plus)
# data_omics = identifyTFs(data_omics)
# data_omics = enrichPWs(data_omics)
# setwd(system.file("extdata/Genelists", package = "pwOmics"))
# data_omics = identifyPWTFTGs(data_omics, only_enriched = FALSE)
# getDS_TFs(data_omics)
# ## End(Not run)

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