On Mon, Dec 8, 2014 at 9:18 PM, Valerie Obenchain <voben...@fredhutch.org> wrote:
> (Resend - last message didn't post to the list.) > > OK, sounds good. In 1.13.18 I've deprecated VRangesScanVcfParam() and > changed the signature of readVcfAsVRanges() to use ScanVcfParam(). > > If at some point we want to revise the defaults for ScanVcfParam() to a > minimal subset I'm fine with that. > It might be time to have a GUI widget that helps people construct a ScanVcfParam. > > Valerie > > > > On 12/08/14 13:32, Michael Lawrence wrote: > >> The reason why 'y' and 'z' are different is the same reason why >> readVcfAsVRanges exists. It was meant to be a convenience so that users >> could get the minimal information needed into the VCF. But maybe that >> was just being too helpful, and the user ends up confused. So I agree >> with Julian that we should just drop VRangesScanVcfParam and have >> readVcfAsVRanges just be an alternative syntax to as(readVcf(), >> "VRanges"). >> >> Michael >> >> On Mon, Dec 8, 2014 at 10:48 AM, Valerie Obenchain >> <voben...@fredhutch.org <mailto:voben...@fredhutch.org>> wrote: >> >> Michael, how would you feel about dropping VRangesScanVcfParam? I'm >> open to changing the defaults in ScanVcfParam; the current 'read all >> fields' default is probably not the best approach. >> >> Valerie >> >> >> >> On 12/04/2014 02:47 AM, Julian Gehring wrote: >> >> Hi, >> >> Can we harmonize the default parameters for =ScanVcfParam= and >> =VRangesScanVcfParam=? It even seems that we could drop >> =VRangesScanVcfParam= since it is mainly a wrapper for >> =ScanVcfParam=. >> >> Currently, the defaults for importing fields from a VCF are: >> >> ScanVcfParam: fixed = character(), info = character(), geno = >> character() >> >> VRangesScanVcfParam: fixed = "ALT", info = NA, geno = "AD" >> >> When using >> >> readVcfAsVRanges(vcf_path, genome_name) >> >> with default parameters, that yields a VRanges object only the >> 'AD' >> metadata column. If 'AD' is not present in the VCF file (which is >> perfectly fine because it is not essential), it throws a warning. >> >> My main motivation behind all of this is that I would expect >> >> x = readVcf(vcf_path, genome_name) >> y = as(x, "VRanges") >> >> and >> >> z = readVcfAsVRanges(vcf_path, genome_name) >> >> to give an equal object. I added some code below to make the >> case more >> concrete: >> >> library(VariantAnnotation) >> >> vcf_path = system.file("extdata", "ex2.vcf", >> package="VariantAnnotation") >> >> ## read VRanges (implicit conversion) >> z = readVcfAsVRanges(vcf_path, "ncbi37") >> >> ## read VCF, convert to VRanges (explicitly) >> x = readVcf(vcf_path, "ncbi37") >> y = as(x, "VRanges") >> >> ## harmonize it >> vr_param = VRangesScanVcfParam(fixed = character(), info = >> character(), geno = character()) >> >> z2 = readVcfAsVRanges(vcf_path, "ncbi37", param = vr_param) >> >> all.equal(unname(y), unname(z2)) >> >> >> Best >> Julian >> >> _________________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> https://stat.ethz.ch/mailman/__listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> >> > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
