pwOmics (version 1.4.0)

getTFIntersection: Get TF intersection for the omics data on the different time points.

Description

Get TF intersection for the omics data on the different time points.

Usage

getTFIntersection(data_omics, tp_prot, tp_genes, only_enriched = FALSE)

Arguments

data_omics
OmicsData object.
tp_prot
numeric integer defining protein timepoint measurement chosen for comparison.
tp_genes
numeric integer defining gene/transcript timepoint measurement chosen for comparison.
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) character vector of transcription factor IDs identified in both upstream and downstream analysis 2) protein time point 3) gene/transcript time point.

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)
# data_omics = identifyRsofTFs(data_omics, only_enriched = FALSE,
# noTFs_inPW = 1, order_neighbors = 10)
# data_omics = identifyPWTFTGs(data_omics, only_enriched = FALSE)
# getTFIntersection(data_omics, 4,4,only_enriched = TRUE)
# ## End(Not run)

Run the code above in your browser using DataCamp Workspace