VEP-class: Class VEP

In griffithlab/GenVisR: Genomic Visualizations in R

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

griffithlab/GenVisR documentation built on May 14, 2024, 12:40 a.m.