Description Usage Arguments Value Examples
View source: R/pwOmics_get_functions.R
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.
1 2 | getProteinIntersection(data_omics, tp_prot, tp_genes, updown = FALSE,
phospho = TRUE)
|
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. |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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)
getProteinIntersection(data_omics, tp_prot = 4, tp_genes = 4,
updown = FALSE, phospho = TRUE)
## End(Not run)
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