readBGENToMatrixByGene {seqminer} | R Documentation |
Read a gene from BGEN file and return a genotype matrix
readBGENToMatrixByGene(fileName, geneFile, geneName)
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 |
genotype matrix
http://zhanxw.com/seqminer/ for online manual and 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")