hyperGtest {ChIPpeakAnno} | 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

### 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)

[Package ChIPpeakAnno version 3.12.7 Index]