Description Usage Arguments Value Examples
View source: R/pwOmics_upstream_analysis.R
This function identifies the upstream transcription factors of the provided gene IDs.
1 | identifyTFs(data_omics)
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data_omics |
OmicsData object. |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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)
## End(Not run)
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