getAdFromVcf | R Documentation |
get the Allele depth from vcf
getAdFromVcf(file, keep = NULL, chromosome = NULL)
file |
vcf file path |
keep |
a vector store high confidence site, format should be "chr_1" |
chromosome |
vector, which chromosome to use if it is NULL, all chromosome will be include in analysis |
a binmapr object with AD and related information
Zhougeng Xu
library(vcfR)
data(vcfR_test)
orig_dir <- getwd()
temp_dir <- tempdir()
setwd( temp_dir )
write.vcf( vcfR_test, file = "test.vcf.gz" )
ad <- getAdFromVcf("test.vcf.gz")
ad
# return is full of NA, because the origin vcf don't have INFO/AD
setwd( orig_dir )
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