Exact test for equality of allele frequencies in males and females
EAFExact uses a Fisher Exact test to compare allele frequencies
in males and females for variants with k alleles (k >= 2).
EAFExact(m, f, verbose = TRUE, ...)
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 |
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.
pval |
p-value |
tab |
table with allele counts |
Jan Graffelman jan.graffelman@upc.edu
# # 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)
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