ChIPpeakAnno (version 3.6.4)

hyperGtest: 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

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

Details

see phyper for details

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)