How can I do the simple task of subsetting a VCF object to only the PASS entries (without converting to a user-friendly VRanges object)? subset looks like the function to use, but the description of it sounds a lot like developer documentation rather than end-user documentation and the Examples section has no example of its usage. I don't know how to use it. I also thought about filtering at the importation stage using ScanVcfParam, but the which parameter can only be a GRanges object, not a condition like FILTER == PASS.

After running

example(readVcf)

I have an object (note that it has two dimensions, with 5 variants and 3 samples)

> vcf
class: CollapsedVCF
dim: 5 3
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DFrame with 1 column: AF
info(header(vcf)):
      Number Type  Description
   AF A      Float Allele Frequency
geno(vcf):
  SimpleList of length 1: HQ
geno(header(vcf)):
      Number Type    Description
   HQ 2      Integer Haplotype Quality

As suggested by the display, the FILTER field is accessible as rowRanges(), and then with, e.g., $FILTER

> rowRanges(vcf)
GRanges object with 5 ranges and 5 metadata columns:
                 seqnames          ranges strand | paramRangeID            REF
                    <Rle>       <IRanges>  <Rle> |     <factor> <DNAStringSet>
       rs6054257       20           14370      * |        geneA              G
    20:17330_T/A       20           17330      * |        geneA              T
       rs6040355       20         1110696      * |        geneB              A
  20:1230237_T/.       20         1230237      * |        geneB              T
       microsat1       20 1234567-1234569      * |        geneB            GTC
                                ALT      QUAL      FILTER
                 <DNAStringSetList> <numeric> <character>
       rs6054257                  A        29        PASS
    20:17330_T/A                  A         3         q10
       rs6040355                G,T        67        PASS
  20:1230237_T/.                           47        PASS
       microsat1             G,GTCT        50        PASS
  -------
  seqinfo: 1 sequence from hg19 genome
> rowRanges(vcf)$FILTER
[1] "PASS" "q10"  "PASS" "PASS" "PASS"

We'd like to keep features (variants) with rowRanges(vcf)$FILTER == "PASS", and all samples, expecting 4 rows and 3 column

> vcf[ rowRanges(vcf)$FILTER == "PASS",]
class: CollapsedVCF
dim: 4 3
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DFrame with 1 column: AF
info(header(vcf)):
      Number Type  Description
   AF A      Float Allele Frequency
geno(vcf):
  SimpleList of length 1: HQ
geno(header(vcf)):
      Number Type    Description
   HQ 2      Integer Haplotype Quality

Is that what you were looking for?

subset is a convenience around the elements that occur exactly once on each row

> subset(vcf, FILTER == "PASS")
class: CollapsedVCF
dim: 4 3
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DFrame with 1 column: AF
info(header(vcf)):
      Number Type  Description
   AF A      Float Allele Frequency
geno(vcf):
  SimpleList of length 1: HQ
geno(header(vcf)):
      Number Type    Description
   HQ 2      Integer Haplotype Quality