cnv.plot: Create a copy number and structural variant plot.

In jjellis/GenomicVis: Genomic Visualisation Routines

Description

Creates a figure containing structural variants (large INDELs, translocations), B allele frequency, copy number changes and log R ratios. Each of these data types is supplied as a data.frame so the function is agnostic about the source of the data.

Usage

cnv.plot(chr, snps, segments, svs)

Arguments

chr	The chromosome to process
snps	A data.frame containing the following columns Chr LRR BAF Position
segments	A data.frame containing the following columns Chr Copy LRR
svs	A data.frame containing the following columns Chr1 Chr2 Pos1 Pos2 Type Support

Details

While the function is agnostic about where the data comes from, the GenomicVis package provides functions and examples to obtain data from Illumina SNP-Chips that have been processed with GenomeStudio and GAP and structural variants from BreakDancer. Ultimately, however, this data may come from any source (or even multiple sources) so long as it is presented to the function via the three standadised data.frames.

foo

a foo bar

Value

none

Author(s)

Jonathan Ellis <[e-mail]>

Examples

data(SNPExample)
data(CNVExample)
data(SVExample)
cnv.plot('18', SNPExample, CNVExample, SVExample)

jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.