Description Usage Arguments Examples
Function to load vcf file for a particular gene and transcrit, given a transcript object as returned by VEP EPI. Requires: VariantAnnotation, BiocGenerics
1 2 | loadVcfFileForGene(vcfFile, transcript, includeFilteredSites = F, n = -1,
refVersion = "GRCh37", returnGenotypes = F)
|
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. |
1 | exacdata<- loadVcfFileForGene('exac.vcf',transcript)
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