getAAFrequencies {midasHLA}

R Documentation

Calculate amino acid frequencies

Description

getAAFrequencies calculates amino acid frequencies in amino acid data frame.

Usage

getAAFrequencies(aa_variation)

Arguments

aa_variation

Amino acid variation data frame as returned by hlaToAAVariation.

Details

Both gene copies are taken into consideration for frequencies calculation, frequency = n / (2 * j) where n is the number of amino acid occurrences and j is the number of samples in aa_variation.

Value

Data frame with each row holding specific amino acid position, it's count and frequency.

Examples

aa_variation <- hlaToAAVariation(MiDAS_tut_HLA)
getAAFrequencies(aa_variation)

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