track.CNV.DGVsupp: DGV supporting variant parser

Description Usage Arguments Value Author(s) References See Also

Description

This function constructs track.CNV objects from free annotation files provided by the Database of Genomic Variants.

It is designed to parse supporting variants, as opposed to track.CNV.DGV provided by Rgb which is designed to parse DGV Variants.

Usage

1
  track.CNV.DGVsupp(file, name = "DGV CNV (supporting variants)", quiet = FALSE, ...)

Arguments

file

Single character value, the path to the raw file to parse. See the 'References' section below.

name

Single character value, the name field for the track.table object.

quiet

Single logical value, whether to print diagnostic messages or not.

...

Further arguments are passed to the class constructor, as a result most of the handled arguments are track.table arguments. Consider notably .organism and .assembly for track annotation.

Value

Return a track.CNV object.

Author(s)

Sylvain Mareschal

References

Example of raw file (human assembly 'hg19') : http://dgv.tcag.ca/dgv/docs/GRCh37_hg19_supportingvariants_2014-10-16.txt

See Also

track.table-class, track.CNV-class, track.CNV.DGV


cghRA documentation built on May 2, 2019, 3:34 a.m.