GMS-class {GenVisR} | R Documentation

## 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`

[Package GenVisR version 1.26.0 Index]