readVCFToMatrixByRange: Read a gene from VCF file and return a genotype matrix

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Read a gene from VCF file and return a genotype matrix

Description

Read a gene from VCF file and return a genotype matrix

Usage

readVCFToMatrixByRange(fileName, range, annoType)

Arguments

fileName	character, represents an input VCF file (Bgzipped, with Tabix index)
range	character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index
annoType	character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty.

Value

genotype matrix

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
cfh <- readVCFToMatrixByRange(fileName, "1:196621007-196716634", "Nonsynonymous")

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.