facopy (version 1.6.0)

facopyPlot: Plot a Genome-Wide Overview of Association Results

Description

The function plots alteration frequencies by genomic feature, broken down by variable value (if the variable is discrete). It also allows to plot relevant alteration frequencies within a specified external dataset.

Usage

facopyPlot(fad, alteration, varName, db = NULL)

Arguments

fad

facopyInfo object with a certain study's facopy data.

alteration

A character describing the kinds of alteration to include. It should be one of the following: - amplifications All amplifications (CN>2). - deletions All deletions (CN<2). -="" loh All loss of heterozygosity (LOH), regardless of copy number. - cnas All copy number alterations (CN<>2). - any Any kind of alteration. - all Any kind of alteration, same as any. - onlygain Only non-LOH amplifications. - someloss All deletions plus LOH alterations.

varName

A character indicating the variable of interest within the facopyInfo object. Call summary on your facopyInfo object to see the names of defined variables.

db

An optional string representing the name of a database whose data will be overlaid in the output plot. Typically, the format is "[database]_[dataset]". The total amplification plus deletion frequencies will be displayed unless alteration indicates either amplification or deletion. In such cases, only the matching alterations are displayed.

Value

A plot is generated in the graphics device. Nothing is returned.

Details

Alterations in the selected external database, if selected, are depicted as grey overlaid bars.

Examples

data(myStudy) # load example study

facopyPlot(myStudy, "amp", "stage", db="gsk_colon")