EAFExact: Exact test for equality of allele frequencies in males and...

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Exact test for equality of allele frequencies in males and females

Description

EAFExact uses a Fisher Exact test to compare allele frequencies in males and females for variants with k alleles (k >= 2).

Usage

EAFExact(m, f, verbose = TRUE, ...)

Arguments

m	vector or triangular matrix with male genotype counts
f	vector or triangular matrix with female genotype counts
verbose	print output (TRUE) or not (FALSE)
...	additional arguments for fisher.test

Details

For bi-allelic autosomal variants the genotype counts can be supplied as vectors ((AA,AB,BB) for males, and (AA,AB,BB) for females). For X-chromosomal bi-allelic variants the genotype counts can also supplied as vectors ((A,B) for males, and (AA,AB,BB) for females). For multi-allelic autosomal variants male and genotype counts can be supplied as vectors (AA,AB,AC,BB,BC,CC,...) or as a triangular matrix, where matrix rows and colums are labelled with the allele name (A,B,C,...). For multi-allelic X-chromosomal variants, male genotype counts must be supplied as a vector (A,B,C,...) and female genotype counts must be supplied as a triangular matrix. See the examples below.

Value

pval	p-value
tab	table with allele counts

Author(s)

Jan Graffelman [e-mail]

See Also

fisher.test

Examples

#
# bi-allelic autosomal
#

m <- c(AA=60,AB=96,BB=44) 
f <- c(AA=44,AB=97,BB=59) 
EAFtest <- EAFExact(m,f)

#
# bi-allelic X-chromosomal
#

males   <- c(A=392, B=212)
females <- c(AA=275, AB=296, BB=80)
EAFtest <- EAFExact(males,females,verbose=TRUE)

#
# tri-allelic autosomal
#

males   <- c(AA=20,AB=52,AC=34,BB=17,BC=51,CC=26)
females <- c(AA=28,AB=55,AC=33,BB=18,BC=50,CC=16)
EAFtest <- EAFExact(males,females,verbose=TRUE)

#
# tri-allelic X-chromosomal
#

males   <- c(A=15,B=17,C=24) 
females <- toTriangular(c(AA=4,AB=2,AC=13,BB=6,BC=19,CC=4)) 
EAFtest <- EAFExact(males,females,verbose=TRUE)

HardyWeinberg documentation built on May 7, 2022, 5:05 p.m.