count.function

Counts the number of each dNTP in each position of an aligned barcode matrix.

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

count.function function

<dl> <dt>nucleotides</dt>
<dd>A matrix of aligned DNA barcode sequences. DNA sequences should start at the third column of the matrix, while the first column contains a unique specimen identifier and the second column contains the species name.</dd> <dt>spec.no</dt>
<dd>The number of specimen/sequences in the nucldeotide matrix.</dd> <dt>seqlength</dt>
<dd>The length of the nucleotide sequences.</dd></dl>

Arguments

Taryn B. T. Athey and Paul D. McNicholas

Author

Nucleotide Count — count.function

<dl>

 <dt>nucleotides</dt>
<dd>A matrix of aligned DNA barcode sequences. DNA sequences should start at the third column of the matrix, while the first column contains a unique specimen identifier and the second column contains the species name.</dd>

 <dt>spec.no</dt>
<dd>The number of specimen/sequences in the nucldeotide matrix.</dd>

 <dt>seqlength</dt>
<dd>The length of the nucleotide sequences.</dd>

</dl>

count.function: Nucleotide Count

Description

Usage

Value

Arguments

Author

Examples