facopyPlot {facopy} | R Documentation

## 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.

### Details

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

### Value

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

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

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

[Package facopy version 1.13.0 Index]