GmapSnps-class: Class '"GmapSnps"'

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

Description

This class represents a set of SNPs (single nucleotide polymorphisms) for use with GMAP and GSNAP (typically for SNP-tolerant alignment.)

Usage

GmapSnps(snps, directory, name = snps, create = FALSE, ...)

Arguments

snps	A path to a VCF file
directory	The directory to create the IIT files used by GMAP and GSNAP
name	If provided, the name to give the database of SNPs. If not provided, defauts to the snps argument.
create	If the directory provided in the directory argument does not exist, create it.
...	Additional arguments to be passed to the SNPs replacement method.

Objects from the Class

##TODO: doc these args Objects can be created by calls of the form GmapSnps(snps, directory, name, create).

Accessors

name(x): returns the name of the GmapSnps object

directory(x): returns the GmapGenomeDirectory that is the parent of the directory containing the index files for this GmapSnps object.

Methods

directory

signature(x = "GmapSnps"): ...

Author(s)

Michael Lawrence

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.