hyperGtest: hypergeometric test

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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

See Also

phyper, getEnrichedGO

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)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.