hyperGtest

0th

Percentile

hypergeometric test

hypergeometric test with lower.tail = FALSE used by getEnrichedGO

Keywords
internal
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

References

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

See Also

phyper, getEnrichedGO

Aliases
  • hyperGtest
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)
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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