pwOmics (version 1.4.0)

enrichPWs: Pathway enrichment - downstream analysis.

Description

This function does pathway enrichment for pathways determined via identifyPWs function.

Usage

enrichPWs(data_omics, method = "BH", alpha = 0.05, ...)

Arguments

data_omics
OmicsData object.
method
correction method for multiple testing correction as specified in p.adjust documentation; default is Benjamini & Hochberg correction.
alpha
significance level for pathway enrichment; default is alpha = 0.05.
...
further input parameters for multiple comparison adjustment.

Value

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.

Examples

Run this code
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"),
TFtargetdatabase = c("chea"))

data_omics = readTFdata(data_omics)
data_omics_plus = readPWdata(data_omics,
loadgenelists = "Genelists")

## Not run: 
# data_omics = identifyPWs(data_omics_plus)
# data_omics = identifyTFs(data_omics)
# data_omics = enrichPWs(data_omics)
# ## End(Not run)

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