It would be nice to have a high-level GUI that allowed the user to specify a query and then showed a sample of the query result, perhaps along with some plotting capabilities. Julian is somewhat close to something like that, I think.
On Tue, Dec 9, 2014 at 2:50 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > > > 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
