plotCNVs: Gviz plot of CNVs

In isglobal-brge/R-GADA: Genome Alteration Detection Algorithm (GADA)

Description

This function plots the CNVs of each sample in a given genomic region and annotates the genes using Gviz

Usage

plotCNVs(x, range, genome="hg19", drawGenes=FALSE, group, 
         col.cnvs =c("darkgreen", "darkblue"), mosaic = FALSE)

Arguments

x	an object of class 'cnvGRanges' obtained after applying 'getCNVs' function
range	a 'GRanges' object indicating the genomic region to be depicted
genome	the reference genome. The default is 'hg19'
drawGenes	should genes be showed in the plot? The default is FALSE
group	a grouping variable to provide CNVs for each level. Only to levels are allowed. Not required.
col.cnvs	color of gain and loses. Default is darkgreen for gains and darkblue for loses.
col.group	color of grouping variable. Used when 'group' is provided. Default are tomato and lightblue.
mosaic	argument not relevant for R-GADA (see MAD package)

Value

This function returns an Gviz plot showing the CNVs of each sample in a given genomic region. Gains are in green color, while loses are printed in blue.

References

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples". BMC Bioinformatics, 2010;11:380.

See Also

getCNVs

Examples

 ## Not run: 
  See the vignette
 
## End(Not run) 

isglobal-brge/R-GADA documentation built on May 24, 2019, 5:03 a.m.