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

Description Usage Arguments Details Value Note Author(s) References Examples

View source: R/bindcadd_snv.R

Description

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

Usage

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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 <stvjc@channing.harvard.edu>

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

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 ## Not run: 
  data(ebicat_2020_04_30)
  g2 = as(ebicat_2020_04_30, "GRanges")
 # would need to lift over here 
  bindcadd_snv( g2[which(seqnames(g2)=="chr2")][1:20] )
  
## End(Not run)

gwascat documentation built on Nov. 8, 2020, 11:08 p.m.