seqminer (version 6.7)

readBGENToListByGene: 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 genes, and each elements has specified vcfColumn, vcfinfo, vcfIndv

See Also

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

Examples

# NOT RUN {
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")
# }

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