GMS-class: Class GMS

In griffithlab/GenVisR: Genomic Visualizations in R

Class GMS

Description

An S4 class for Genome Modeling System annotation files, under development!!!

Usage

GMS(path, data = NULL, version = 4, verbose = FALSE)

Arguments

path	String specifying the path to a GMS annotation file. Can accept wildcards if multiple GMS annotation files exist (see details).
data	data.table object storing a GMS annotation file. Overrides "path" if specified.
version	String specifying the version of the GMS files, Defaults to version 4.
verbose	Boolean specifying if progress should be reported while reading in the GMS files.

Details

When specifying a path to a GMS annotation file the option exist to either specify the full path to an annotation file or to use wildcards to specify multiple files. When specifying a full path the initalizer will check if a column named "sample" containg the relevant sample for each row exists. If such a column is not found the initalizer will assume this file corresponds to only one sample and populate a sample column accordingly. Alternatively if multiple files are specified at once using a wildcard, the initalizer will aggregate all the files and use the file names minus any extension top populate sample names. The version defaults to 4 which is the default value of the GMS annotator. This value will need to be changed only if files were created using a different GMS annotator version.

Slots

path

Character string specifying the paths of the GMS files read in.

version

Numeric value specifying the version of the GMS annotation files.

gmsObject

gms object which inherits from gms_Virtual class.

See Also

Waterfall

MutSpectra

griffithlab/GenVisR documentation built on April 18, 2024, 7:06 p.m.