cash-writeVCF: RA Method: Write genotype data to VCF format

In tpbilton/GUSbase: Genotyping Uncertainty with Sequencing Data: Base Package

RA Method: Write genotype data to VCF format

Description

Method for converting allele count data in an RA object back to VCF format.

Usage

RAobj$writeVCF(snpsubset=NULL, indsubset=NULL, file="GUSbase", IDuse=NULL)

Arguments

snpsubset

Integer vector giving the indices of the SNPs to retain in the VCF file

indsubset

Integer vector giving the indices of the samples to retain in the VCF file

file

Character giving the name of the VCF file to be written

IDuse

Character vector specifying alternative samples names. Useful for anonymizing sample IDs.

Author(s)

Timothy P. Bilton

See Also

RA

Examples

file <- simDS()
RAfile <- VCFtoRA(file$vcf)
subset <- readRA(RAfile, snpsubset = 10:30)

## write the subset of the data back to VCF format
subset$writeVCF(file = "subset")

tpbilton/GUSbase documentation built on March 8, 2024, 1:35 p.m.