VEP-class {GenVisR} | R Documentation

## Class VEP

### Description

An S4 class for Variant Effect Predictor input, under development!!!

### Usage

    VEP(path, data = NULL, version = "auto", verbose = FALSE)

### Arguments

`path` | String specifying the path to a VEP annotation file. Can accept wildcards if multiple VEP 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 VEP files, Defaults to auto which will look for the version in the header.
`verbose` | Boolean specifying if progress should be reported while reading in the VEP files.

### Details

When specifying a path to a VEP 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 to populate sample names.

### Slots

`path`

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

`version`

  Numeric value specifying the version of VEP used.

`vepObject`

  vep object which inherits from VEP_Virtual class.

### See Also

`Waterfall`

`MutSpectra`

[Package GenVisR version 1.12.1 Index]