Search
Question: about the use of subsetByFilter()
0
gravatar for Bogdan
17 months ago by
Bogdan490
Palo Alto, CA, USA
Bogdan490 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 17 months ago by Martin Morgan ♦♦ 21k • written 17 months ago by Bogdan490
3
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

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

subsetByFilter(vcf, filter=FilterRules(list(AFADfilter=AFADfilter)))
ADD COMMENTlink modified 17 months ago • written 17 months ago by Martin Morgan ♦♦ 21k

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 17 months ago by Bogdan490
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: 120 users visited in the last hour