Description Usage Arguments Value Examples
View source: R/pwOmics_integration_functions.R
This function determines the regulated downstream structures of a selected phosphoprotein at a specified time point.
1 | findSignalingAxes(data_omics, phosphoprot, tpDS)
|
data_omics |
OmicsData object. |
phosphoprot |
character specifying the name of the phosphoprotein that is selected as the starting point for downstream analysis. |
tpDS |
integer specifying the time point considered for downstream analysis of phosphoprotein data . |
list of downstream pathways identified for this time point of phosphoprotein measurement with sublists containing information about the transcription factor, the regulation, the target genes of these transcription factors and the matching transcripts.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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"))
setwd(system.file("extdata/Genelists", package = "pwOmics"))
## Not run:
data_omics_plus = identifyPR(data_omics_plus)
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)
SYK_axis = findSignalingAxes(data_omics,phosphoprot = "SYK", tpDS = 2)
## End(Not run)
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