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

In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

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

Details

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

Value

GRanges instance with additional fields as obtained in the CADD resource

Note

This software developed in part with support from Genentech, Inc.

Author(s)

VJ Carey <[e-mail]>

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

 if (interactive()) {
  data(ebicat37)
  g2 = as(ebicat37, "GRanges")
  bindcadd_snv( g2[which(seqnames(g2)=="chr2")][1:20] )
  }

vjcitn/gwascat documentation built on May 5, 2019, 7:59 p.m.