facopy (version 1.6.0)

facopyEnrichment: Gene-set Enrichment Analysis

Description

Performs gene-set enrichment analysis of cancer copy number data, based on a gene table, a facopyInfo object and the correlations between gene copy number and expression data.

Usage

facopyEnrichment(fad, geneTable, cor, outFolder,  pvalThr = 0.05, corThr = 0.1, plotThr=0.001)

Arguments

fad

facopyInfo object with a certain study's facopy data.

geneTable

A table with the format of facopy function's output, containing at least the columns regarding feature name, p-value and chromosome arm.

cor

A list generated by a call to calculateCor, containing information on correlation between gene copy number and expression data.

outFolder

The folder to which to write the enrichment results.

pvalThr

Maximum p-value required to consider a gene to be significantly associated.

corThr

Minimum R2 required to consider a gene's copy number and expression to be sufficiently correlated.

plotThr

Pathways from Biocarta, KEGG and Reactome with lower p-values than this integer will have their graphs plotted in the output folder.

Value

The input gene table is returned with correlation values attached, ordered by p-value and then by R2.

Details

Only use this function and calculateCor if you selected some kind of gene collection as genomic features.

Examples

data(myStudy) # load example study

# then perform an association analysis
# genes = facopy(myStudy, "amp", "stage")

# calculate expression-CN correlations
# eCor = calculateCor(myStudy, "mrna_merged_median_Zscores", "coadread_tcga_pub")

# and run facopy enrichment
# facopyEnrichment(myStudy, genes, eCor, "~/myFolder/stageAmpEnrichment")