gettpIntersection: Get omics data intersection on the three levels. Get...

In MarenS2/pwOmics_maren: Pathway-based data integration of omics data

Description

Get omics data intersection on the three levels.

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

Usage

gettpIntersection(data_omics, updown = FALSE, phospho = TRUE)

Arguments

data_omics	OmicsData object.
updown	boolean value; TRUE in case up- and downregulation should be checked individually for intersection. Type of checking is defined with parameter 'phospho'.
phospho	boolean value; TRUE in case up- and downregulation should be checked based on provided downstream phosphoprotein influence from identifyPR function; FALSE in case up- and downregulation should be checked for without phosphoprotein database knowledge. Default is TRUE.

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

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("userspec"))
data_omics = readPhosphodata(data_omics, 
phosphoreg = system.file("extdata", "phospho_reg_table.txt", 
package = "pwOmics")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics"))
data_omics_plus = readPWdata(data_omics, 
loadgenelists = system.file("extdata/Genelists", package = "pwOmics"))
## Not run: 
data_omics_plus = identifyPR(data_omics_plus)
setwd(system.file("extdata/Genelists", package = "pwOmics"))
data_omics = identifyPWs(data_omics_plus)
data_omics = identifyTFs(data_omics)
data_omics = identifyPWTFTGs(data_omics)
data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10)
gettpIntersection(data_omics, updown = FALSE, phospho = TRUE)

## End(Not run)

MarenS2/pwOmics_maren documentation built on May 6, 2019, 3:27 p.m.