plotRecurrentRegions: Plot recurrent CNV regions

In CNVRanger: Summarization and expression/phenotype association of CNV ranges

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")

CNVRanger documentation built on Dec. 12, 2020, 2 a.m.