Search
Question: about the use of subsetByFilter()
0
gravatar for Bogdan
23 months ago by
Bogdan530
Palo Alto, CA, USA
Bogdan530 wrote:

Dear Martin, and all, 

would like to ask for an advice about the use of the function subsetByFilter(vcf, filter). 

I have the following piece of R code that is working (below) -- thanks Martin for suggestions !

vcf <- readVcf("AML_out.vcf.bgzip",genome="hg38")

AFADfilter = function(x) {
            af <- geno(x)$AF[,"TUMOR"] > 0.05
            ad <- sum(as(geno(x)$AD[,"TUMOR"], "List")) >= 5
            af & ad
                         }

z <- vcf[AFADfilter(vcf)]
writeVcf(z,"output.vcf")

However, if I want to use the function subsetByFilter(), there is an error message :

subsetByFilter(vcf, filter=AFADfilter)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘subsetByFilter’ for signature ‘"CollapsedVCF", "function"’
vcf
ADD COMMENTlink modified 23 months ago by Martin Morgan ♦♦ 22k • written 23 months ago by Bogdan530
3
gravatar for Martin Morgan
23 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

The filter argument is supposed to be a FilterRules object, so

subsetByFilter(vcf, filter=FilterRules(list(AFADfilter=AFADfilter)))
ADD COMMENTlink modified 23 months ago • written 23 months ago by Martin Morgan ♦♦ 22k

I see, it is a same rule as before, when filtering on VCF files, and not working on VCF objects. Thanks a lot Martin, have a happy, warm and fruitful week !

ADD REPLYlink written 23 months ago by Bogdan530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 226 users visited in the last hour