fasta.read

Reads in fasta files and converts into sequence 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

fasta.read function

<dl> <dt>file</dt>
<dd>A fasta file to be read in.</dd> <dt>seqlength</dt>
<dd>Length of sequence.</dd> <dt>pos1</dt>
<dd>The position within the fasta title of the unique specimen identifier. By default pos1 = 1.</dd> <dt>pos2</dt>
<dd>The position within the fasta title of the species name. By default pos2 = 3.</dd></dl>

Arguments

Taryn B. T. Athey and Paul D. McNicholas

Author

Read Fasta Files — fasta.read

<dl>

 <dt>file</dt>
<dd>A fasta file to be read in.</dd>

 <dt>seqlength</dt>
<dd>Length of sequence.</dd>

 <dt>pos1</dt>
<dd>The position within the fasta title of the unique specimen identifier. By default pos1 = 1.</dd>

 <dt>pos2</dt>
<dd>The position within the fasta title of the species name. By default pos2 = 3.</dd>

</dl>

fasta.read: Read Fasta Files

Description

Usage

Value

Arguments

Author