plotZoom: Zoom In to Plot a Chromosome Arm or a Genomic Feature

In facopy: Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

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")

facopy documentation built on May 2, 2018, 2:30 a.m.