minorAlleleFrequency: Minor Allele Frequency (MAF) Detection
In obenlan2/Lab-9: Minor Allele Frequency (MAF) Detection

Description Usage Arguments Value Author(s) Examples

View source: R/SNPfreq_functions.R

A set of functions that allow for detection of SNP MAF, allow for filtering SNPs by MAF, and creating a histogram of SNP MAF.

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

`SNPmat`	Matrix of SNPs to used in the function.
`minMAF`	Minimun MAF value of SNPs you'd like to keep. Default value is set to 0.05 but can be set to other values as needed

`minorAlleleFrequency`	Returns a vector of MAFs.
`filterSNPs`	Returns a matrix in the same format as the inputed matrix but with columns removed for SNPs with very rare alleles.
`mafHis`	Draws a histogram of SNP MAFs.

Olivia Obenland

SNPmat <- matrix(c(2,4,6,8,10,12,14,16,18,3,6,9,12,15,18), nrow = 5, ncol = 3)

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