VEP-class: Class VEP
In GenVisR: Genomic Visualizations in R

Description Usage Arguments Details Slots See Also

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

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

`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.

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.

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.

Waterfall

MutSpectra

GenVisR documentation built on Dec. 28, 2020, 2 a.m.