cocohet: Test for compound heterozygote effects
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) References Examples

Detecting rare recessive and compound heterozygote alleles in genome wide association.

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  cocohet(data, trait, window, return_all_result = TRUE,
    makePlot = FALSE, test = "CHI2",
    min_expected_cut_off = -1)

`data`	Genotype data for analysis. Object of class `snp.data`
`trait`	Vector with binary trait data. Object of class `integer` or `numeric`.
`window`	Number of SNPs on the "right" of a given SNP which are used in analysis with a SNP. Object of class `integer`
`return_all_result`	If FALSE then return only a vector where each element is a chisq obtained as a maximum chisq between a given SNP and SNPs on the right within a window. If TRUE then return also a matrix where chisq's for all tests are stored. Object of class `logical`
`makePlot`	whether the Manhattan-type plot should be produced (TRUE or FALSE)
`test`	Name of the test to be performed. Available tests are "CHI2", "YATES" (chi2 with Yates correction), and "FISHER". Object of class `character`
`min_expected_cut_off`	In case this is >=0 and test is NOT Pearson's chisq test then Pearson's chisq test (!) is performed only for SNPs which produce acontingency table where the expected number of subjects in each field is >min_expected_cut_off. Otherwise the specified test is performed. Object of class `integer` or `numeric`

The function is an inplementation of the method aimed to detect a gene-phenotype association caused by recessive and compound heterozygote genotype states of multiple rare variants at a particular gene locus. This method is described in 'Detecting Low Frequent Loss-of-Function Alleles in Genome Wide Association Studies with Red Hair Color as Example'; Fan Liu, Maksim V. Struchalin, Kate van Duijn, Albert Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and Manfred Kayser. PLoS ONE 6(11): e28145. doi:10.1371/journal.pone.0028145

The three tests are implemented: Pearson's chi-square test, Pearson's chi-square test with Yates correction, Fisher exact test. In case when the input parameter min_expected_cut_off is <0 the choosen in the input parameter "test" test is performed. If min_expected_cut_off >= 0 then always Pearson's chi-square test is performed exept of the cases when expected number of subjects in a field of contingency table is <min_expected_cut_off. In this case the test choosen in the input parameter test is performed.

A list is returned.

Maksim Struchalin

Fan Liu, Maksim V. Struchalin, Kate van Duijn, Albert Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and Manfred Kayser. Detecting Low Frequent Loss-of-Function Alleles in Genome Wide Association Studies with Red Hair Color as Example'. PLoS ONE 6(11): e28145. doi:10.1371/journal.pone.0028145

require(GenABEL.data)
data(srdta)
chis2_nocorrection <- cocohet(data=gtdata(srdta),
trait=phdata(srdta)$bt, window=3, test="CHI2")

Loading required package: MASS
Loading required package: GenABEL.data
Running Pearson's chi-square test.
Starting analysis...
All 833 snps are done.
[1] "The top snp has name rs5017,is located in chromosome 1, position 1329000"