pwOmics (version 1.4.0)

gettpIntersection: Get omics data intersection on the three levels.

Description

Get intersection for the omics data on all three levels (proteins, TFs, genes) on corresponding time points.

Usage

gettpIntersection(data_omics, only_enriched = FALSE)

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 FALSE.

Value

list with three elements: 1) protein intersection 2) transcription factor intersection 3) gene intersection each element contains a list with overlapping time points of both upstream and downstream analyses.

Examples

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