subvcf: Subset of VCF data
In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description Usage Arguments Value Author(s) See Also Examples

To obtain a subset of a vcf object data.

1 2	subvcf(vcf, CHR = NULL, POS = NULL, CHRPOS=NULL, samples = NULL, TF = NULL)

`vcf`	A vcf object data.
`CHR`	Chromosome. To get the subset of input vcf data based on specified chromosome(s).
`POS`	Position. To get the subset of input vcf data based on specified positions.
`CHRPOS`	Position within a chromosome separated by colon.
`samples`	To specify sample(s) of interest.
`TF`	A vector of logical values. To define which of the corresponding positions will be extracted.

A vcf object returned.

Qiang Hu

filtervcf

vcffile <- system.file("extdata", "1151HZ0001.flt.vcf", package="VPA")
vcfdata <- read.vcf(vcffile)

#extract calls in position 1:985999
subvcf(vcfdata, CHRPOS="1:985999")

#extract calls by TF
tf <- c(rep(TRUE, 10), rep(FALSE, length(vcfdata$POS)-10))
subvcf(vcfdata, TF=tf)