getProteinIntersection: Get protein intersection for the omics data on the different...

In pwOmics: Pathway-based data integration of omics data

Description

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

The timepoints or measurement names for comparison have to be defined in tp_prot and tp_genes as given in the readOmics function.

Usage

getProteinIntersection(data_omics, tp_prot, tp_genes, updown = FALSE,
  phospho = TRUE)

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.
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) character vector of protein IDs identified in both upstream and downstream analysis 2) protein time point 3) gene/transcript time point.

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)
data_omics = identifyTFs(data_omics)
data_omics = identifyPWTFTGs(data_omics)
data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10)
getProteinIntersection(data_omics, tp_prot = 4, tp_genes = 4, 
updown = FALSE, phospho = TRUE)

## End(Not run)

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