aa.count.function

Counts the number of each amino acid in each positino of the barcode.

Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.

Taryn T. Athey

Frequency Matrix Approach for Assessing Very Low Frequency
Variants in Sequence Records

aa.count.function function

<dl> <dt>aminoAcids</dt>
<dd>A matrix of barcode amino acid sequences.</dd> <dt>seqlength</dt>
<dd>Length of the amino acid sequences.</dd></dl>

Arguments

Taryn B. T. Athey and Paul D. McNicholas

Author

Amino Acid Count — aa.count.function

<dl>

 <dt>aminoAcids</dt>
<dd>A matrix of barcode amino acid sequences.</dd>

 <dt>seqlength</dt>
<dd>Length of the amino acid sequences.</dd>

</dl>

aa.count.function: Amino Acid Count

Description

Usage

Value

Arguments

Author

Details

Examples