minorAlleleFrequency: Function to calculate Minor Allele Frequency from SNPs
In lucasmr2/SNPfreqfun: SNP Allele Frequency Estimation and Utilities

Description Usage Arguments Value Note Author(s) Examples

This package calculates minor allele frequencies

minorAlleleFrequency(SNPmat)

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

`SNPmat`
`minMAF`	This sets the minimum minor allele frequency, commonly 0.05

minorAlleleFrequency returns a vector of allele frequencies filterSNPs returns a SNP matrix in the same format as SNPmat but with columns removed for SNPs with very rare alleles mafHis draws a histogram plot of the MAF and does not return anything

Most of this code was provided by Lindsay Clark

Lucas Roberts

SNPmat <- matrix(1:9, nrow = 3, ncol = 3)

function (SNPmat) 
{
    maf <- colMeans(SNPmat, na.rm = TRUE)/2
    common <- which(maf > 0.5)
    maf[common] <- 1 - maf[common]
    return(maf)
  }