addCodonLine {HLAtools}

Add an 'AA codon' Line to Alignments When Missing.

Description

Modifies cDNA alignment objects that are missing "AA codon" lines to include these lines in the correct location with the correct codon position information.

Usage

addCodonLine(cDNAalign, firstPos, afterLine = 8, codons = 25)

Arguments

cDNAalign

A matrix of cDNA alignment lines, generated from an alignment file that is missing "AA codon" lines.

firstPos

A numeric value identifying the position number of the transcript's N-terminal codon, based on a complete cDNA alignment in another release.

afterLine

A numeric value identifying the number of the line below the first "cDNA" line in the alignment. The default value is 8.

codons

A numeric value identifying the number of codons in each line of the nucleotide alignment. The default value is 25.

Value

A complete cDNA alignment data frame that includes "AA codon" rows.

Note

For internal HLAtools use.