getClinSig: Get clinical significance by querying a tabix indexed bed...

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

Description

Get clinical significance by querying a tabix indexed bed file

Usage

getClinSig(df, db.path, verbose = T)

Arguments

df	A bed file like dataframe containing the columns: chrom, pos, ref, alt
db.path	Path to a tabix indexed bed file with the clinical significance annotations (e.g. from ClinVar). This bed file should contain the columns (in this order): chrom, pos, ref, alt, clinsig, id. However, it should not have colnames.
verbose	Show progress messages?

Value

A character vector of the clinical significance annotations

luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.