loadVcfFileForRegion: loadVcfFileForRegion

In gdelangel/genomicRTools: Genomic R Tools

Description

Function to load vcf file for a particular genomic region

Usage

loadVcfFileForRegion(vcfFile, chr, start, end, includeFilteredSites = F,
  n = -1, refVersion = "GRCh37", returnGenotypes = F)

Arguments

vcfFile	File name to load
chr	Chromosome/contig to load
start	Initial genomic position to load
end	Final genomic position to load
includeFilteredSites	Return filtered-out sites (i.e. sites marked with anything other than PASS on vcf). Defaults to FALSE
n	Max number of records to load. Set to -1 for no limit.
refVersion	Reference version. Defaults to "GRCh37".
returnGenotypes	Return genotype data. Default to FALSE.

Examples

exacdata<- loadVcfFileForRegion('exac.vcf',"1",12345600,13345600)

gdelangel/genomicRTools documentation built on May 16, 2019, 11:14 p.m.