exactHWE: Hardy-Weinberg Equilibrium testing
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Value Author(s) See Also Examples

This function performs exact Hardy-Weinberg Equilibrium testing (using Fisher's Test) over a selection of SNPs. It also counts genotype, calculates allele frequencies, and calculates inbreeding coefficients.

exactHWE(genoData, 		
         scan.exclude = NULL,
         geno.counts = TRUE,
         snpStart = NULL,
         snpEnd = NULL,
         block.size = 5000, 
         verbose = TRUE,
         permute = FALSE)

`genoData`	a `GenotypeData` object
`scan.exclude`	a vector of scanIDs for scans to exclude
`geno.counts`	if `TRUE` (default), genotype counts are returned in the output data.frame.
`snpStart`	index of the first SNP to analyze, defaults to first SNP
`snpEnd`	index of the last SNP to analyze, defaults to last SNP
`block.size`	number of SNPs to read in at once
`verbose`	logical for whether to print status updates
`permute`	logical indicator for whether to permute alleles before calculations

HWE calculations are performed with the HWExact function in the GWASExactHW package.

For the X chromosome, only female samples will be used in all calculations (since males are excluded from HWE testing on this chromosome). The X chromosome may not be included in a block with SNPs from other chromosomes. If the SNP selection includes the X chromosome, the scan annotation of genoData should include a "sex" column.

Y and M and chromsome SNPs are not permitted in the SNP selection, since the HWE test is not valid for these SNPs.

If permute=TRUE, alleles will be randomly shuffled before the HWE calculations. Running permutation can yield the expected distribution of p-values and corresponding confidence intervals.

a data.frame with the following columns

`snpID`	the snpIDs
`chr`	chromosome SNPs are on

If geno.counts=TRUE:

`nAA`	number of AA genotypes in samples
`nAB`	number of AB genotypes in samples
`nBB`	number of BB genotypes in samples
`MAF`	minor allele frequency
`minor.allele`	which allele ("A" or "B") is the minor allele
`f`	the inbreeding coefficient
`pval`	exact Hardy-Weinberg Equilibrium (using Fisher's Test) p-value. `pval` will be `NA` for monomorphic SNPs (`MAF=0`).

Ian Painter, Matthew P. Conomos, Stephanie Gogarten, Adrienne Stilp

HWExact

library(GWASdata)
data(illuminaScanADF)

# run only on YRI subjects
scan.exclude <- illuminaScanADF$scanID[illuminaScanADF$race != "YRI"]

# create data object
gdsfile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
gds <- GdsGenotypeReader(gdsfile)
genoData <-  GenotypeData(gds, scanAnnot=illuminaScanADF)
chr <- getChromosome(genoData)

# autosomal SNPs
auto <- range(which(is.element(chr, 1:22)))
hwe <- exactHWE(genoData, scan.exclude=scan.exclude, 
                snpStart=auto[1], snpEnd=auto[2])

# permutation
perm <- exactHWE(genoData, scan.exclude=scan.exclude, 
                snpStart=auto[1], snpEnd=auto[2],
                permute=TRUE)

# X chromosome SNPs must be run separately since they only use females
Xchr <- range(which(chr == 23))
hweX <- exactHWE(genoData, scan.exclude=scan.exclude, 
                 snpStart=Xchr[1], snpEnd=Xchr[2])

close(genoData)