[Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]

Michael Lawrence lawrence.michael at gene.com
Tue Mar 13 03:29:58 CET 2018

You could look at the rtracklayer API. For example, using gets functions
like track<-() and range<-() to set track and region may be more natural to
R users. Then again, if there were endomorphic functions add_track() and
set_range(), the API would support chaining. There should be no need to
explicitly construct a track; just rely on dispatch and class semantics,
i.e., passing a VCF object to add_track() would create a variant track

On Mon, Mar 12, 2018 at 5:20 PM, Paul Shannon <
paul.thurmond.shannon at gmail.com> wrote:

> Gabe and Levi made a good case for supporting GRanges in IGV.   Looking at
> the GenomicRanges vignettes, it appears that many of Herve’s introductory
> examples have GC content as the mcols column of interest.   Would that be a
> good test and demo for IGV?  Or perhaps some other genomic quantity,  one
> for which sample data is already present in some Bioconductor package’s
> extdata?
> The IGV VCF track now works, using GenomicRanges and VariantAnnotation.
> It might be of interest, maybe lead to more useful suggestions which would
> be good for me to hear at this stage.   Here is a code chunk using default
> parameters for colors, track height and etc.  Homozygous non-reference
> calls are rendered in light blue, heterozygous in dark blue, reference in
> gray.
> library(IGV)
> library(VariantAnnotation)
> igv <- IGV(portRange=9000:9020)
> setGenome(igv, “hg19")
> setBrowserWindowTitle(igv, “VCF demo”)
> f <- system.file("extdata", "chr22.vcf.gz", package=“VariantAnnotation”)
> chrom <- “22"
> start <- 50586118
> end   <- 50633733
> rng <- GRanges(seqnames=chrom, ranges=IRanges(start=start, end=end))
> vcf.sub <- readVcf(f, "hg19", param=rng)
> track <- VariantTrack(“chr22-tiny", vcf.sub)
> displayTrack(igv, track)
> showGenomicRegion(igv, sprintf("chr22:%d-%d", start-1000, end+1000))
> Suggestions?
> > On Mar 9, 2018, at 4:15 AM, Levi Waldron <lwaldron.research at gmail.com>
> wrote:
> >
> > Definitely +1 for supporting GenomicRanges, including what's in genome()
> and mcols(). There's a demo of an rtracklayer -> GRanges -> UCSC
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