getHGMDData: getHGMDData

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

getHGMDData(geneName, user = "hgmd", password = "hgmd",
  host = "192.168.99.100", port = "3306", dbname = "hgmd")

Arguments

geneName	Gene name to load
user	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<- getHGMDData('CFTR')

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