Description Usage Arguments Value Examples
View source: R/pwOmics_read_data.R
This function reads in phosphoprotein downstream regulation information from a txt file.
1 | readPhosphodata(data_omics, phosphoreg)
|
data_omics |
OmicsData object. |
phosphoreg |
txt file with 2 columns, first providing gene names, second giving -1/1 annotation whether downstream regulation of phosphoprotein is inhibiting or activating, respectively. |
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; PhosphoD containing optionally phosphoprotein downstream regulation annotation.
1 2 3 4 5 6 7 8 | 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"))
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