seqminer (version 2.0)

readVCFToMatrixByGene: Read a gene from VCF file and return a genotypes matrix

Description

Read a gene from VCF file and return a genotypes matrix

Usage

readVCFToMatrixByGene(fileName, geneFile, geneName,
    annoType)

Arguments

fileName

charactr, 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")