annotatedAlignment: Construct an 'annotatedAlignment'.

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

Description

Construct an ‘annotatedAlignment’.

Usage

annotatedAlignment(alnpath, annopath, type, ...)

Arguments

alnpath	Path to a directory containing mercator segments, a single file in mfa (multi fasta) or maf (multiple alignment file) format containing the genome aligment.
annopath	Path to annotation files.
type	Type of annotation. Supported file types are gff, ptt, ftb (NCBI feature table), genbank/gbk, and table (custom tab-delimted annotation files, minimally containing start and end values).
...	Optionally features (default: CDS, RNA), seqid (sequence identifier, e.g. NCBI accession numbers), and sep.

See Also

mercator, alignSegments, annotatedAlignment.

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