hyperGtest {ChIPpeakAnno} | R Documentation |
hypergeometric test with lower.tail = FALSE used by getEnrichedGO
hyperGtest(alltermcount, thistermcount, totaltermInGenome, totaltermInPeakList)
alltermcount |
a list with two variables: GOterm and GOcount which is GO terms and corresponding counts in the whole genome |
thistermcount |
a list with two variables: GOterm and GOcount which is GO terms and corresponding counts in the peak list |
totaltermInGenome |
number of total GO terms in the whole genome |
totaltermInPeakList |
number of total GO terms in the peak list |
see phyper for details
a list with 6 variables
thisterm |
GO term |
thistermcount |
count of this GO term in the peak list |
thistermtotal |
count of this GO term in the whole genome |
pvalue |
pvalue of the hypergeometric test |
totaltermInPeakList |
number of total GO terms in the peak list |
totaltermInGenome |
number of total GO terms in the whole genome |
internal function not intended to be used directly by users
Lihua Julie ZHu
Johnson, N. L., Kotz, S., and Kemp, A. W. (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley
phyper, getEnrichedGO
goList= c("GO:0000075", "GO:0000082","GO:0000082","GO:0000122", "GO:0000122","GO:0000075","GO:0000082","GO:0000082", "GO:0000122","GO:0000122","GO:0000122","GO:0000122", "GO:0000075", "GO:0000082","GO:000012") alltermcount = list(GOterm=c("GO:0000075", "GO:0000082", "GO:000012", "GO:0000122"), GOcount=c(100, 200, 10, 10)) thistermcount = getUniqueGOidCount(goList) totaltermInPeakList = 15 totaltermInGenome = 1000 hyperGtest(alltermcount,thistermcount, totaltermInGenome, totaltermInPeakList)