getClinvarData: getClinvarData

In gdelangel/genomicRTools: Genomic R Tools

Description

Function to load from HGMD MySQL database. Assumes data schema as published by HGMD. Requires RMySQL package

Usage

getClinvarData(clinvarFile, transcript, useTableData)

Arguments

clinvarFile	Gene name to load
transcript	VEP transcript object or list. Needs to contain 'id', 'seq_region_name','start' and 'end' elements
password	Return filtered-out sites (i.e. sites marked with anything other than PASS on vcf). Defaults to FALSE
host	Max number of records to load. Set to -1 for no limit.
port	Reference version. Defaults to "GRCh37".
dbname	Reference version. Defaults to "GRCh37".

Examples

hgmddata<- getClinvarData('clinvar.vcf',transcript)

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