make_gsea_overlap_igraph: this function takes a bioConductor EList (eg....
In ptvan/Pmisc: Phu's Misc Functions

Description Usage Arguments Value Examples

View source: R/make_gsea_overlap_igraph.R

this function takes a bioConductor EList (eg. voom-transformed RNASeq counts) GSEA output matrix from limma's camera() and a user-specified geneSet and create an igraph graph where the nodes are gene lists and the edge weight is how many expressed genes are common between the gene lists Phu T. Van, FHCRC 2017, w/ substantial help and input from C.Murie & V.Voillet

1	make_gsea_overlap_igraph(expressionList, cameraMat, geneSets, verbose = FALSE)

`expressionList`	a matrix of gene expression values
`cameraMat`	matrix contain output from CAMERA
`geneSets`	a list of list of geneIds
`verbose`	Boolean whether to print out progress

table of genes' mean expression values for each group

## Not run: 
vDat <- voom(exprs(eDat), design=designMat, plot=FALSE, lib.size=libNorm)
res <- camera(vDat, setsIndices, design=designMat, contrast=cons[i], sort=TRUE)
geneSets <- geneIds(getGmt(gmtFile))
n <- make_gsea_igraph(vDat, res, geneSets)
plot(n, edge.width=E(n)$overlap*.1, vertex.color="white", vertex.label.cex=0.5)

## End(Not run)