GmapGenomeDirectory-class: Class '"GmapGenomeDirectory"'

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

Description

The GmapGenomeDirectory class stores a path to a directory containing a one or more genome-specific subdirectories, each represented by a GmapGenome. Inside those directories are the files that the GMAP suite of tools uses for alignment, tallying, and other operations. This class is typically used to create a GmapGenome object. The default directory is ~/.local/share/gmap, following the freedesktop.org XDG standard.

Constructor

GmapGenomeDirectory(path = getDefaultGmapGenomePath(), create = FALSE): Creates an object pointing to the directory at path, creating it if it does not yet exist and create is TRUE.

Methods

path(object): gets the path to the genome directory.

genome(x): gets the names of the genomes in the directory.

Author(s)

Michael Lawrence

See Also

GmapGenome-class

Examples

gmapGenomePath <- file.path(getwd(), "newGmapGenomeDirectory")
gmapGenomeDirectory <- GmapGenomeDirectory(gmapGenomePath, create = TRUE)

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