matchGrToVcfObj

#library(VariantAnnotation)
#library(data.table)
#devtools::load_all("d:/source/cqsR")
#devtools::load_all(".")

library(cqsR)

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fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
vcf <- VariantAnnotation::expand(x = vcf, row.names = TRUE)

variantsTable=data.frame(chr="22", start=c(50300078,50300085), end=c(50300078,50300102), score=1:2)
variantsTableGr=makeGRangesFromDataFrame(variantsTable)
#matchGrToVcfObj(variantsTableGr,vcf)
readVcfAndMatchGr(fl,variantsTableGr)

## [1] "Reading vcf: 10376"

##    chr    start      end REF ALT FILTER   AF
## 1:  22 50300078 50300078   A   G   PASS 0.34
## 2:  22 50300086 50300086   C   T   PASS 0.01

Untitled

matchGrToVcfObj

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