plotBar {facopy} | R Documentation

## Overview of Alterations by Chromosome Arm

### Description

The function plots amplification and deletion frequencies by chromosome arm, as well as LOH frequencies

### Usage

    plotBar(fad, byFeature = TRUE, sel = NULL, selColors = NULL,
            ylim = c(-1, 1), baseColor = "black",
            varName = NULL, value = NULL)

### Arguments

`fad` | `facopyInfo` object with a certain study's `facopy` data.
`byFeature` | A logical. If `TRUE`, arm frequencies are calculated as the mean alteration frequencies across genomic features in each arm. If `TRUE`, they are calculated as the mean proportion of altered base pairs in each arm.
`sel` | A character vector with the chromosome arms that will be highlighted using the colors in `selColors`. Example: `c("1q","9p")`.
`selColors` | A vector of colors with the same length as the parameter `sel`. Each color in the vector will be used for the selected chromosome arm in the same position within `sel`.
`ylim` | A two integer vector indicating frequency limits in the plot. Deletion frequency is indicated with a negative number. Default is `c(-1,1)`.
`baseColor` | Base color of the triangles that indicate frequencies in the plot. Default is `"black"`.
`varName` | Either `NULL` or a character indicating the variable of interest within the `facopyInfo` object. Call `summary` on your `facopyInfo` object to see the names of defined variables. If `NULL`, the frequencies across all samples are plotted. Otherwise, only samples with the variable value in the parameter `value` are selected for the computation. In this latter case, only categorical variables are allowed.
`value` | Value that the samples should have for the selected variable. Only these samples are selected for the frequency calculation.

### Details

Amplification frequencies are depicted by chromosome arm over the horizontal line, while deletion frequencies appear below it. The frequencies of alterations with LOH are depicted as smaller triangles.

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

    # select some chromosome arms to highlight
    myArms = c("8q","13q","20q","8p","18q")
    myColors = c(rainbow(15)[1:3], rainbow(15)[10:11])

    plotBar(myStudy, TRUE, myArms, myColors, ylim=c(-0.5,1))

[Package facopy version 1.13.0 Index]