minorAlleleFrequency: MINOR ALLELE FREQUENCY FUNCTIONS

In mrweber2/usefulRcode: SNP Allele Frequency Functions

Description

minorAlleleFrequency will calculate the minor allele frequency. filterSNPs will filter out SNPs by an allele frequency threshold. mafHist will plot a histogram of minor allele frequencies.

Usage

minorAlleleFrequency(SNPmat)
filterSNPs(SNPmat, minMAF = 0.05)
mafHist(SNPmat)

Arguments

SNPmat	matrix of SNP frequencies
minMAF	filter out alleles below this allele frequency threshold
mafHist	matrix of SNP frequencies

Value

minorAlleleFrequency	Returns a vector of allele frequencies.
filterSNPS	Returns a matrix filtered by minor allele frequency, in the same format as SNPmat.
mafHist	Draws a histogram of allele frequencies.

Examples

mat <- matrix(runif(30), nrow=10, ncol=3)

maf <- minorAlleleFrequency(mat)
filteredMat <- filterSNPs(mat, minMAF = 0.05)
mafHist(mat)

mrweber2/usefulRcode documentation built on May 21, 2019, 4:06 a.m.