readVCFToMatrixByGene {seqminer} | R Documentation |
Read a gene from VCF file and return a genotype matrix
Description
Read a gene from VCF file and return a genotype matrix
Usage
readVCFToMatrixByGene(fileName, geneFile, geneName, annoType)
Arguments
fileName |
character, represents an input VCF 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 |
annoType |
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty. |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readVCFToMatrixByGene(fileName, geneFile, "CFH", "Synonymous")
[Package seqminer version 9.4 Index]