identifyPWs: Identify pathway IDs and pathway names of differentially...

In pwOmics: Pathway-based data integration of omics data

Description

This function identifies the pathways of the differentially abundant phosphoproteins dependent on the chosen database. Requires rBiopaxParser package. Takes a lot of time for a high number of proteins and/or if all databases are chosen. First, chosen databases are loaded, then new internal pathway IDs are generated. Afterwards the genelists of the different databases are loaded or generated, depending on the loadgenelists option. After pathway identification for the reference time point, also pathway identification for different time points is performed. Pathway ID mapping takes some time, especially for such big databases as reactome, so use savegenelists and loadgenelists for easier and faster usage...

Usage

identifyPWs(data_omics_plus)

Arguments

data_omics_plus

output list of readPWdata function; first element contains an OmicsData object, secons element the genelist data corresponding to the selected pathway database.

Value

OmicsData object: list of 4 elements (OmicsD, PathwayD, TFtargetsD, Status); OmicsD containing omics data set + results (after analysis); PathwayD containing selected pathway databases + biopax model; TFtargetsD containing selected TF target gene databases + TF target gene data.

Examples

## Not run: 
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.newupdown")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics.newupdown"))
data_omics_plus = readPWdata(data_omics,  
loadgenelists = system.file("extdata/Genelists", package = "pwOmics.newupdown"))

## End(Not run)
## Not run: 
data_omics_plus = identifyPR(data_omics_plus)
setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))
data_omics = identifyPWs(data_omics_plus)

## End(Not run)

pwOmics documentation built on Nov. 8, 2020, 4:55 p.m.