readVCFToMatrixByRange {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
readVCFToMatrixByRange(fileName, range, annoType)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index |
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")
cfh <- readVCFToMatrixByRange(fileName, "1:196621007-196716634", "Nonsynonymous")
[Package seqminer version 9.4 Index]