inst/demos/bamFile.R
In PriceLab/igvR: igvR: integrative genomics viewer
library(igvR)
bamFile <- system.file(package="igvR", "extdata", "tumor.bam")
file.exists(bamFile)
igv <- igvR(quiet=FALSE)
setGenome(igv, "hg38")
little.region <- GRanges(seqnames = "21", ranges = IRanges(10399760, 10401370))
showGenomicRegion(igv, "chr21:10,397,772-10,403,883")
param <- ScanBamParam(which=little.region, what=scanBamWhat())
x <- readGAlignments(bamFile, use.names=TRUE, param=param)
track <- GenomicAlignmentTrack("bam demo", x, visibilityWindow=2000000, trackHeight=500)
displayTrack(igv, track)
PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.
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library(igvR)
bamFile <- system.file(package="igvR", "extdata", "tumor.bam")
file.exists(bamFile)
igv <- igvR(quiet=FALSE)
setGenome(igv, "hg38")
little.region <- GRanges(seqnames = "21", ranges = IRanges(10399760, 10401370))
showGenomicRegion(igv, "chr21:10,397,772-10,403,883")
param <- ScanBamParam(which=little.region, what=scanBamWhat())
x <- readGAlignments(bamFile, use.names=TRUE, param=param)
track <- GenomicAlignmentTrack("bam demo", x, visibilityWindow=2000000, trackHeight=500)
displayTrack(igv, track)
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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