hyperGtest: hypergeometric test
In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

hyperGtest

R Documentation

hypergeometric test

Description

hypergeometric test with lower.tail = FALSE used by getEnrichedGO

Usage

hyperGtest(alltermcount, thistermcount, totaltermInGenome, totaltermInPeakList)

Arguments

`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

Details

see phyper for details

Value

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

Note

internal function not intended to be used directly by users

Author(s)

Lihua Julie ZHu

References

Johnson, N. L., Kotz, S., and Kemp, A. W. (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley

Examples


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)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.