Profling a gene list against gene sets

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Description

number is the number of overlapping genes between the gene list and the gene set.

Usage

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geneListProfile(gs, glist, threshold = 10)

Arguments

gs

gene sets, use prepackaged or user loaded

glist

gene list loaded by user

threshold

specify the mininum number of overlapping genes in a gene set to output. This is to avoid displaying gene sets with very few overlapping genes. For each gene set, if the number of overlapping genes is smaller than the threshold, the set of overlapping genes will be combined to a gene set labeled "Others"

Value

labels

the labels of the gene sets

sizes

the number of overlapping genes of gene sets against gene list

symbols

the gene symbols of overlapping genes

Author(s)

Xutao Deng

Examples

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data(goslim.human.BP)
glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")
r<-geneListProfile(goslim.human.BP, glist, threshold=1)
labels<-sub("_", "__", r$labels) #remove the GO id labels for display, optional
labels<-sub(".*__", "", labels)
pie(r$sizes,labels=labels, main="GO Slim Biological Process Mapping")