bindcadd_snv {gwascat} | R Documentation

## 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

### 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

     ## 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)

[Package gwascat version 2.24.0 Index]