afx: Function to compute X-chromosomal allele frequencies

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

Function to compute X-chromosomal allele frequencies

Description

Function afx computes the allele frequency for a vector or matrix of X-chromosomal genotype counts or frequencies.

Usage

afx(x)

Arguments

x	a vector or matrix with X-chromosomal counts or compositions. x must have five elements or columns.

Details

Function afx calculates the A allele frequency for the given order of X-chromosomal genotype counts (A,B,AA,AB,BB). The genotypes must be supplied this order. Use maf to calculate the minor allele frequency and more flexible coding.

Value

a vector with allele frequencies

Author(s)

Jan Graffelman ([e-mail])

See Also

maf, af

Examples

#
# A simulated random X-chromosomal marker
#
X <- as.vector(rmultinom(1,100,c(0.3,0.2,0.1,0.15,0.25)))
X <- X/sum(X)
print(X)
print(afx(X))
#
# 
#
rs5968922 <-  c(A=392, B=212, AA=275, AB=296, BB=80)
afx(rs5968922)
#
#
#
y <- c(C=337, G=129, CC=277, CG=209, GG=48) 
afx(y)
#
# Calculated allele frequencies (p) for a matrix of X-chromosomal genotype counts.
#
X <- HWData(nm=10,n=1000,x.linked=TRUE)
X
p <- afx(X)
p

HardyWeinberg documentation built on May 29, 2024, 6:17 a.m.