readBGENToMatrixByGene: Read a gene from BGEN 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 BGEN file and return a genotype matrix

Description

Read a gene from BGEN file and return a genotype matrix

Usage

readBGENToMatrixByGene(fileName, geneFile, geneName)

Arguments

fileName	character, represents an input BGEN 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

Value

genotype matrix

See Also

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

Examples

fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readBGENToMatrixByGene(fileName, geneFile, "CFH")

seqminer documentation built on Sept. 2, 2023, 9:08 a.m.