plotZoom {facopy} | R Documentation

## Zoom In to Plot a Chromosome Arm or a Genomic Feature

### Description

The function shows the selected alterations either in a chromosome arm or near a genomic feature, color-coded by variable value.

### Usage

    plotZoom(fad, what = c("feature", "arm"), name,
             alteration, varName, margin = 0)

### Arguments

`fad` | `facopyInfo` object with a certain study's `facopy` data.
`what` | Charcter indicating whether to plot selected alterations either near a genomic feature or in a chromosome arm. Default is `feature`.
`name` | Name of the genomic feature or chromosome arm of interest. Examples: `"MIRN181A2"`, `"14q"`.
`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. Bars representing alterations will be colored according to the classification of the corresponding samples in such variable. Call `summary` on your `facopyInfo` object to see the names of defined variables.
`margin` | If parameter `what` is `"feature"`, a margin downstream and upstream of the genomic feature to consider when searching for overlapping alterations.

### Details

One line per sample in the study is displayed in the case of chromosome arms, whereas only those samples with alterations are displayed in the case of genomic features.

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

    plotZoom(myStudy, "feat", "RAD51L1", "amp", "stage")

    plotZoom(myStudy, "arm", "8p", "del", "stage")

[Package facopy version 1.13.0 Index]