readBGENToMatrixByRange: 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

readBGENToMatrixByRange(fileName, range)

Arguments

fileName	character, represents an input BGEN file (Bgzipped, with Tabix index)
range	character, a text indicating which range in the BGEN file to extract. e.g. 1:100-200, 1-based index

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")
cfh <- readBGENToMatrixByRange(fileName, "1:196621007-196716634")

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