mtAAF: mtAAF function

In mtDNA-BU/ANNOmtDNA: Annotation of mtDNA sequence variations

mtAAF function

Description

Derivation of alternative allele fraction (AAF).

Usage

mtAAF(allele, freq, method = "maxAA")

Arguments

allele	a character matrix (16569 x N) provided by the user. Rows correspond to loci and columns correspond to subjects. This matrix contains the alleles of each subject at each locus. The matrix must contain subject ID as the column names. "/" is used to delimited different allele calls in a locus.
freq	a character matrix (16569 x N) provided by the user. Rows correspond to loci and columns correspond to subjects. This matrix contains the allele fractions of the corresponding allele matrix. The matrix must contain subject ID as the column names. "/" is used to delimited the allele fractions.
method	the method to compute AAF for the case of multiple alternative alleles. The default method "maxAA" computes AAF as the maximum of frequencies of corresponding alternative alleles; and the alternative method "allAA" computes AAF as 1 minus the frequency of reference allele

Value

AAF, a numeric matrix (16569 x N). Rows correspond to loci and columns correspond to subjects. It contains subject ID as the column names, and the AAFs of all 16569 mtDNA loci for each subject.

Examples

## Not run: 
## Read input data
allele_file <- "allele.csv"
freq_file   <- "freq.csv"

allele <- as.matrix( read.csv(file=allele_file, sep=","))
freq   <- as.matrix( read.csv(file=freq_file, sep=","))

aaf=mtAAF(allele, freq)

## End(Not run)

mtDNA-BU/ANNOmtDNA documentation built on Aug. 11, 2022, 1:46 p.m.