codon.clean.msa: Clean an alignment for codon analysis

Description Usage Arguments Value Note Author(s)

View source: R/msa.R

Description

Clean an alignment for codon analysis

Usage

1
codon.clean.msa(x, refseq = NULL, strand = "+")

Arguments

x

An object of type msa

refseq

The name of the reference sequence to be used. If given, strip all columns which contain gaps in refseq. Once this is done, alignment should be in frame. If refseq==NULL then alignment should be in frame as it is sent in (no gaps are stripped).

strand

Either "+" or "-". If "-", reverse complement the alignment.

Value

An object of type msa. It will be the same as the original msa, with the following modifications:

Note

If the input msa (x) is stored as a pointer, its value will be changed to the return value of the function.

Author(s)

Melissa J. Hubisz


rphast documentation built on May 1, 2019, 9:26 p.m.