geneListProfile {geneListPie}R Documentation

Profling a gene list against gene sets

Description

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

Usage

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

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")

[Package geneListPie version 1.0 Index]