readBGENToListByGene: 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

readBGENToListByGene(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

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")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readBGENToListByGene(fileName, geneFile, "CFH")

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