loadVcfFileForGene: loadVcfFileForGene

In gdelangel/genomicRTools: Genomic R Tools

Description

Function to load vcf file for a particular gene and transcrit, given a transcript object as returned by VEP EPI. Requires: VariantAnnotation, BiocGenerics

Usage

loadVcfFileForGene(vcfFile, transcript, includeFilteredSites = F, n = -1,
  refVersion = "GRCh37", returnGenotypes = F)

Arguments

vcfFile	File name to load
transcript	VEP transcript object or list. Needs to contain 'id', 'seq_region_name','start' and 'end' elements
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<- loadVcfFileForGene('exac.vcf',transcript)

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