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Plot recurrent CNV regions

Source: R/population_ranges.R
plotRecurrentRegions.Rd

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.

See also

Gviz::plotTracks

Author

Ludwig Geistlinger

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")
#> Warning: 'getMethods' is deprecated.
#> Use 'getMethodsForDispatch(f, TRUE)' instead.
#> See help("Deprecated")
#> Warning: 'getMethods' is deprecated.
#> Use 'getMethodsForDispatch(f, TRUE)' instead.
#> See help("Deprecated")