Description Usage Arguments Examples
Function to load from HGMD MySQL database. Assumes data schema as published by HGMD. Requires RMySQL package
1 | getClinvarData(clinvarFile, transcript, useTableData)
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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". |
1 | hgmddata<- getClinvarData('clinvar.vcf',transcript)
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