readVCFToMatrixByGene: 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

readVCFToMatrixByGene(fileName, geneFile, geneName, annoType)

Arguments

fileName	character, represents an input VCF file (Bgzipped, with Tabix index)
geneFile	character, a text file listing all genes in refFlat format
geneName	character vector, which gene(s) to be extracted
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")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readVCFToMatrixByGene(fileName, geneFile, "CFH", "Synonymous")

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