pwOmics (version 1.4.0)

getUS_PWs: Get upstream pathways of identified transcription factors.

Description

Get upstream pathways of identified transcription factors.

Usage

getUS_PWs(data_omics)

Arguments

data_omics

OmicsData object.

Value

list of length = number of gene/transcript time points, each element containing a list of transcription factors; these transcription factor elements contain data frame with pathway IDs and pathway names.

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"))
## 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 = identifyRsofTFs(data_omics, only_enriched = FALSE,
# noTFs_inPW = 1, order_neighbors = 10)
# getUS_PWs(data_omics)
# ## End(Not run)