readBGENToListByRange: Read information from BGEN file in a given range and return a...

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

Read information from BGEN file in a given range and return a list

Description

Read information from BGEN file in a given range and return a list

Usage

readBGENToListByRange(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

a list of chrom, pos, varid, rsid, alleles, isPhased, probability, sampleId

See Also

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

Examples

fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
cfh <- readBGENToListByRange(fileName, "1:196621007-196716634")

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