facopyEnrichment {facopy} | R Documentation |
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.
facopyEnrichment(fad, geneTable, cor, outFolder, pvalThr = 0.05, corThr = 0.1, plotThr=0.001)
fad |
|
geneTable |
A table with the format of |
cor |
A list generated by a call to |
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. |
Only use this function and calculateCor
if you selected some kind of gene collection as genomic features.
The input gene table is returned with correlation values attached, ordered by p-value and then by R2.
David Mosen-Ansorena
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")