gwascat (version 2.4.2)

bindcadd_snv: bind CADD scores of Kircher et al. 2014 to a GRanges instance

Description

bind CADD scores of Kircher et al. 2014 to a GRanges instance; by default will use HTTP access at UW

Usage

bindcadd_snv(gr, fn = "http://krishna.gs.washington.edu/download/CADD/v1.0/1000G.tsv.gz")

Arguments

gr

query ranges to which CADD scores should be bound

fn

path to Tabix-indexed bgzipped TSV of CADD as distributed at krishna.gs.washington.edu on 1 April 2014

Value

• GRanges instance with additional fields as obtained in the CADD resource

Details

joins CADD fields at addresses that match query; the CADD fields for query ranges that are not matched are set to NA

References

M Kircher, DM Witten, P Jain, BJ O'Roak, GM Cooper, J Shendure, A general framework for estimating the relative pathogenicity of human genetic variants, Nature Genetics Feb 2014, PMID 24487276

Examples

# requires internet access
 data(ebicat37)
 g2 = as(ebicat37, "GRanges")
 bindcadd_snv( g2[which(seqnames(g2)=="chr2")][1:20] )