Description Usage Arguments Value Examples
Calculate GC content in window around a set of variants
1 | variantGCContent(vcf, fasta, windowSize = 100)
|
vcf |
A |
fasta |
A |
windowSize |
An integer representing the window size around each variant to calculate GC content |
A numeric vector giving the GC content for each variant window in the input
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
require(VariantAnnotation)
require(AnnotationHub)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="ALT", geno=c("GT", "GL"), info=c("LDAF"))
vcf = readVcf(fl,"hg19",param=param)
ah = AnnotationHub()
hg19fa = ah$ensembl.release.72.fasta.homo_sapiens.dna.Homo_sapiens.GRCh37.72.dna.toplevel.fa.rz
varGC = variantGCContent(vcf,hg19fa)
plot(density(varGC))
## End(Not run)
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