importAlignment: Import a genome alignment

In gschofl/genoslideR: Create and manipulate multiple genome alignments with annotation.

Description

Import a genome alignment

Usage

importAlignment(alnpath, outfile = NULL)

Arguments

alnpath	Path to the directory containing mercator segments, a single file in ‘mfa’ (multi-fasta) or ‘maf’ (multiple alignment file) format containing the genome aligment.
outfile	if not NULL the alignment is writen to file in multi-fasta format.

Details

If the alignment is provided as a multi-fasta file the each header must contain a map of the orthologous segments in the following format:

GenomeID GenomeLength ChromosomeID:start:end:strand ... ChromosomeID:start:end:strand

where strand is encodes as + or - and GenomeLength is the length of the genomes in the alignment which can be shorter than the length of the original genome.

Value

A DNAStringSet instance.

See Also

mercator.

gschofl/genoslideR documentation built on May 17, 2019, 8:52 a.m.