facopyEnrichment {facopy} | R Documentation

## 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.

### Details

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

### Value

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

### Author(s)

David Mosen-Ansorena

### 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")

[Package facopy version 1.13.0 Index]