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.resea...@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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