plotRecurrentRegions {CNVRanger} | R Documentation

## Plot recurrent CNV regions

### Description

Illustrates summarized CNV regions along a chromosome.

### Usage

    plotRecurrentRegions(regs, genome, chr, pthresh = 0.05)

### Arguments

`regs` | A `GRanges`. Typically the result of `populationRanges` with `est.recur=TRUE`.
`genome` | Character. A valid UCSC genome assembly ID such as 'hg19' or 'bosTau6'.
`chr` | Character. A UCSC-style chromosome name such as 'chr1'.
`pthresh` | Numeric. Significance threshold for recurrence. Defaults to 0.05.

### Value

None. Plots to a graphics device.

### Author(s)

Ludwig Geistlinger

### See Also

`Gviz::plotTracks`

### Examples

    # read in example CNV calls
    data.dir <- system.file("extdata", package="CNVRanger")
    call.file <- file.path(data.dir, "Silva16_PONE_CNV_calls.csv")
    calls <- read.csv(call.file, as.is=TRUE)

    # store in a GRangesList
    grl <- GenomicRanges::makeGRangesListFromDataFrame(calls,
       split.field="NE_id", keep.extra.columns=TRUE)

    # summarize CNV regions
    cnvrs <- populationRanges(grl, density=0.1, est.recur=TRUE)

    # plot
    plotRecurrentRegions(cnvrs, genome="bosTau6", chr="chr1")

[Package CNVRanger version 1.10.3 Index]