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Question: AnnotationHub man page improvements
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5.2 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
About ?AnnotationHub (package version 1.1.8) All the functions whose values are described under "Value" are not described under "Usage". All the functions listed under "Usage" are not described under "Value". The ahinfo (which seems to be a key function for doing things programmatically) is not described under either "usage" or "value". The examples are great though. Best, Kasper [[alternative HTML version deleted]]
modified 5.2 years ago by Marc Carlson7.2k • written 5.2 years ago by Kasper Daniel Hansen6.4k
0
5.2 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
I was wrong about ahinfo. Is there an exposed interface to getting the result of a path, assuming the path is a character vector. I see I can do AnnotationHub:::.getResource(hub, path) with hub an AnnotationHub and path a character vector. Such an interface would be extremely useful. On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > About ?AnnotationHub (package version 1.1.8) > > All the functions whose values are described under "Value" are not > described under "Usage". All the functions listed under "Usage" are not > described under "Value". > > The ahinfo (which seems to be a key function for doing things > programmatically) is not described under either "usage" or "value". > > The examples are great though. > > Best, > Kasper > [[alternative HTML version deleted]]
Hi Kasper, I think you could just do the following: ah[["goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfSt dPkRep1.narrowPeak_0.0.1.RData"]] Instead of using $like usual: ah$goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfStdP kRep1.narrowPeak_0.0.1.RData Does that solve your problem? Marc On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: > I was wrong about ahinfo. Is there an exposed interface to getting the > result of a path, assuming the path is a character vector. I see I can do > AnnotationHub:::.getResource(hub, path) > with hub an AnnotationHub and path a character vector. > > Such an interface would be extremely useful. > > > On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < > kasperdanielhansen at gmail.com> wrote: > >> About ?AnnotationHub (package version 1.1.8) >> >> All the functions whose values are described under "Value" are not >> described under "Usage". All the functions listed under "Usage" are not >> described under "Value". >> >> The ahinfo (which seems to be a key function for doing things >> programmatically) is not described under either "usage" or "value". >> >> The examples are great though. >> >> Best, >> Kasper >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Technically yes, since I can do function(path) { [[(hub, path) } Still, I think it does make sense to have something a bit more standard (I find the [[ to be a bit unusual, but that may be colored by how I program). Retrieving multiple resources in a single call, like paths = names(hub)[1:10] is going to be used a lot, I predict. Kasper On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Kasper, > > I think you could just do the following: > > ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** > wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] > > Instead of using $like usual: > > ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** > wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData > > > Does that solve your problem? > > > Marc > > > > > > > On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: > >> I was wrong about ahinfo. Is there an exposed interface to getting the >> result of a path, assuming the path is a character vector. I see I can do >> AnnotationHub:::.getResource(**hub, path) >> with hub an AnnotationHub and path a character vector. >> >> Such an interface would be extremely useful. >> >> >> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < >> kasperdanielhansen@gmail.com> wrote: >> >> About ?AnnotationHub (package version 1.1.8) >>> >>> All the functions whose values are described under "Value" are not >>> described under "Usage". All the functions listed under "Usage" are not >>> described under "Value". >>> >>> The ahinfo (which seems to be a key function for doing things >>> programmatically) is not described under either "usage" or "value". >>> >>> The examples are great though. >>> >>> Best, >>> Kasper >>> >>> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD REPLYlink written 5.2 years ago by Kasper Daniel Hansen6.4k
Hijacking the thread to discuss TAB completion as well. hub = AnnotationHub() hub$<tab> # looks good, let me try goldenpath hub$goldenpath.<tab> hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] hub$goldenpath.vicPac1.database. ... [14] hub$goldenpath.xenTro ... [34] This is a bit useless, since mostly I see single letters. I would suggest the following First, the names tend to be super long. So don't start the examples with the entire path, like hub$goldenpath.a but perhaps something like "current selection: goldenpath. a.. [59] b.. [110] etc, so that goldenpath is only listed once. That way, the suggestions are shorter and it is clearer what the choices are between (at least I think that is the case) Now, when I go down the list to hub$goldenpath.hg19.encodeDCC.wgEncode I get Possible completions are: hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroadHiston e ... [280] hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAffyExo n ... [107] hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode ... [4] hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage ... [108] hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] But for example, for wgEncodeA, it turns out that there are only two real choices: hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip ... [52] hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase ... [124] but I can't really see this. Anyway, I know this is hard to program, but right now it is a bit hard to explore using the TAB completion. Perhaps this can all be fixed by having more suggestions (there is probably a limited to how many suggestions to show). In this particular case, with this many choices of resources, I guess I would rather have (many) more suggestions than fewer. At the end I just did print(names(hub)) and looked at that, which is probably not what we want. Best, Kasper On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Technically yes, since I can do > > function(path) { > [[(hub, path) > } > > Still, I think it does make sense to have something a bit more standard (I > find the [[ to be a bit unusual, but that may be colored by how I > program). > > Retrieving multiple resources in a single call, like > paths = names(hub)[1:10] > is going to be used a lot, I predict. > > Kasper > > > > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > >> Hi Kasper, >> >> I think you could just do the following: >> >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] >> >> Instead of using $like usual: >> >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData >> >> >> Does that solve your problem? >> >> >> Marc >> >> >> >> >> >> >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: >> >>> I was wrong about ahinfo. Is there an exposed interface to getting the >>> result of a path, assuming the path is a character vector. I see I can >>> do >>> AnnotationHub:::.getResource(**hub, path) >>> with hub an AnnotationHub and path a character vector. >>> >>> Such an interface would be extremely useful. >>> >>> >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < >>> kasperdanielhansen@gmail.com> wrote: >>> >>> About ?AnnotationHub (package version 1.1.8) >>>> >>>> All the functions whose values are described under "Value" are not >>>> described under "Usage". All the functions listed under "Usage" are not >>>> described under "Value". >>>> >>>> The ahinfo (which seems to be a key function for doing things >>>> programmatically) is not described under either "usage" or "value". >>>> >>>> The examples are great though. >>>> >>>> Best, >>>> Kasper >>>> >>>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.2 years ago by Kasper Daniel Hansen6.4k
and, continuing on this important new resource, shouldn't the following work? > class(x) [1] "AnnotationHub" attr(,"package") [1] "AnnotationHub" > x class: AnnotationHub length: 7855 filters: none hubUrl: http://annotationhub.bioconductor.org/ah snapshotVersion: 2.13; snapshotDate: 2013-06-26 hubCache: /Users/stvjc/.AnnotationHub > keys(x, keytype="Description") Enter a frame number, or 0 to exit 1: keys(x, keytype = "Description") 2: keys(x, keytype = "Description") 3: .local(x, keytype, ...) 4: .keys(snapshotUrl(x), keytype) 5: unique(.parseJSON(url)) 6: .parseJSON(url) 7: tryCatch({ tmp <- tempfile() if (getOption("AnnotationHub.debug", FAL 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) 10: value[[3]](cond) i'd also suggest that ahinfo() return an object, not end with a message. > sessionInfo() R version 3.0.1 Patched (2013-06-02 r62857) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII attached base packages: [1] parallel stats graphics grDevices datasets utils tools [8] methods base other attached packages: [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 [7] digest_0.6.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 [7] stats4_3.0.1 XVector_0.1.0 On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Hijacking the thread to discuss TAB completion as well. > > hub = AnnotationHub() > hub$<tab> > # looks good, let me try goldenpath > hub$goldenpath.<tab> > hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] > hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] > hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] > hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] > hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] > hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] > hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] > hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] > hub$goldenpath.vicPac1.database. ... [14] > hub$goldenpath.xenTro ... [34] > > This is a bit useless, since mostly I see single letters. I would suggest > the following > > First, the names tend to be super long. So don't start the examples with > the entire path, like > hub$goldenpath.a > but perhaps something like > "current selection: goldenpath. > a.. [59] > b.. [110] > etc, so that goldenpath is only listed once. That way, the suggestions are > shorter and it is clearer what the choices are between (at least I think > that is the case) > > Now, when I go down the list to > hub$goldenpath.hg19.encodeDCC.wgEncode > > I get > > Possible completions are: > hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] > hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroadHist one ... > [280] > hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] > hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAffyE xon ... > [107] > hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode ... [4] > hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] > hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] > hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage ... [108] > hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] > hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] > > But for example, for wgEncodeA, it turns out that there are only two real > choices: > hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip ... > [52] > hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase ... > [124] > > but I can't really see this. > > Anyway, I know this is hard to program, but right now it is a bit hard to > explore using the TAB completion. Perhaps this can all be fixed by having > more suggestions (there is probably a limited to how many suggestions to > show). In this particular case, with this many choices of resources, I > guess I would rather have (many) more suggestions than fewer. > > At the end I just did > print(names(hub)) > and looked at that, which is probably not what we want. > > Best, > Kasper > > > > On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com> wrote: > > > Technically yes, since I can do > > > > function(path) { > > [[(hub, path) > > } > > > > Still, I think it does make sense to have something a bit more standard > (I > > find the [[ to be a bit unusual, but that may be colored by how I > > program). > > > > Retrieving multiple resources in a single call, like > > paths = names(hub)[1:10] > > is going to be used a lot, I predict. > > > > Kasper > > > > > > > > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > > > >> Hi Kasper, > >> > >> I think you could just do the following: > >> > >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] > >> > >> Instead of using $like usual: > >> > >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData > >> > >> > >> Does that solve your problem? > >> > >> > >> Marc > >> > >> > >> > >> > >> > >> > >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: > >> > >>> I was wrong about ahinfo. Is there an exposed interface to getting the > >>> result of a path, assuming the path is a character vector. I see I can > >>> do > >>> AnnotationHub:::.getResource(**hub, path) > >>> with hub an AnnotationHub and path a character vector. > >>> > >>> Such an interface would be extremely useful. > >>> > >>> > >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < > >>> kasperdanielhansen@gmail.com> wrote: > >>> > >>> About ?AnnotationHub (package version 1.1.8) > >>>> > >>>> All the functions whose values are described under "Value" are not > >>>> described under "Usage". All the functions listed under "Usage" are > not > >>>> described under "Value". > >>>> > >>>> The ahinfo (which seems to be a key function for doing things > >>>> programmatically) is not described under either "usage" or "value". > >>>> > >>>> The examples are great though. > >>>> > >>>> Best, > >>>> Kasper > >>>> > >>>> [[alternative HTML version deleted]] > >>> > >>> ______________________________**_________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >>> Search the archives: http://news.gmane.org/gmane.** > >>> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >>> > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >> Search the archives: http://news.gmane.org/gmane.** > >> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 5.1 years ago by Vincent J. Carey, Jr.6.2k
On Thu, Aug 1, 2013 at 7:39 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > and, continuing on this important new resource, shouldn't the following > work? > >> class(x) > [1] "AnnotationHub" > attr(,"package") > [1] "AnnotationHub" >> x > class: AnnotationHub > length: 7855 > filters: none > hubUrl: http://annotationhub.bioconductor.org/ah > snapshotVersion: 2.13; snapshotDate: 2013-06-26 > hubCache: /Users/stvjc/.AnnotationHub >> keys(x, keytype="Description") > > Enter a frame number, or 0 to exit > > 1: keys(x, keytype = "Description") > 2: keys(x, keytype = "Description") > 3: .local(x, keytype, ...) > 4: .keys(snapshotUrl(x), keytype) > 5: unique(.parseJSON(url)) > 6: .parseJSON(url) > 7: tryCatch({ > tmp <- tempfile() > if (getOption("AnnotationHub.debug", FAL > 8: tryCatchList(expr, classes, parentenv, handlers) > 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) > 10: value[[3]](cond) > This is fixed now. Thanks. Dan > i'd also suggest that ahinfo() return an object, not end with a message. > >> sessionInfo() > R version 3.0.1 Patched (2013-06-02 r62857) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] > en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII > > attached base packages: > [1] parallel stats graphics grDevices datasets utils tools > [8] methods base > > other attached packages: > [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 > [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 > [7] digest_0.6.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 > [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 > [7] stats4_3.0.1 XVector_0.1.0 > > > > On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen < > kasperdanielhansen at gmail.com> wrote: > >> Hijacking the thread to discuss TAB completion as well. >> >> hub = AnnotationHub() >> hub$<tab> >> # looks good, let me try goldenpath >> hub$goldenpath.<tab> >> hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] >> hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] >> hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] >> hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] >> hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] >> hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] >> hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] >> hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] >> hub$goldenpath.vicPac1.database. ... [14] >> hub$goldenpath.xenTro ... [34] >> >> This is a bit useless, since mostly I see single letters. I would suggest >> the following >> >> First, the names tend to be super long. So don't start the examples with >> the entire path, like >> hub$goldenpath.a >> but perhaps something like >> "current selection: goldenpath. >> a.. [59] >> b.. [110] >> etc, so that goldenpath is only listed once. That way, the suggestions are >> shorter and it is clearer what the choices are between (at least I think >> that is the case) >> >> Now, when I go down the list to >> hub$goldenpath.hg19.encodeDCC.wgEncode >> >> I get >> >> Possible completions are: >> hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] >> hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroadHis tone ... >> [280] >> hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] >> hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAffy Exon ... >> [107] >> hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode ... [4] >> hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] >> hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] >> hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage ... [108] >> hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] >> hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] >> >> But for example, for wgEncodeA, it turns out that there are only two real >> choices: >> hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip ... >> [52] >> hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase ... >> [124] >> >> but I can't really see this. >> >> Anyway, I know this is hard to program, but right now it is a bit hard to >> explore using the TAB completion. Perhaps this can all be fixed by having >> more suggestions (there is probably a limited to how many suggestions to >> show). In this particular case, with this many choices of resources, I >> guess I would rather have (many) more suggestions than fewer. >> >> At the end I just did >> print(names(hub)) >> and looked at that, which is probably not what we want. >> >> Best, >> Kasper >> >> >> >> On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < >> kasperdanielhansen at gmail.com> wrote: >> >> > Technically yes, since I can do >> > >> > function(path) { >> > [[(hub, path) >> > } >> > >> > Still, I think it does make sense to have something a bit more standard >> (I >> > find the [[ to be a bit unusual, but that may be colored by how I >> > program). >> > >> > Retrieving multiple resources in a single call, like >> > paths = names(hub)[1:10] >> > is going to be used a lot, I predict. >> > >> > Kasper >> > >> > >> > >> > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> > >> >> Hi Kasper, >> >> >> >> I think you could just do the following: >> >> >> >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** >> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] >> >> >> >> Instead of using $like usual: >> >> >> >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** >> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData >> >> >> >> >> >> Does that solve your problem? >> >> >> >> >> >> Marc >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: >> >> >> >>> I was wrong about ahinfo. Is there an exposed interface to getting the >> >>> result of a path, assuming the path is a character vector. I see I can >> >>> do >> >>> AnnotationHub:::.getResource(**hub, path) >> >>> with hub an AnnotationHub and path a character vector. >> >>> >> >>> Such an interface would be extremely useful. >> >>> >> >>> >> >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < >> >>> kasperdanielhansen at gmail.com> wrote: >> >>> >> >>> About ?AnnotationHub (package version 1.1.8) >> >>>> >> >>>> All the functions whose values are described under "Value" are not >> >>>> described under "Usage". All the functions listed under "Usage" are >> not >> >>>> described under "Value". >> >>>> >> >>>> The ahinfo (which seems to be a key function for doing things >> >>>> programmatically) is not described under either "usage" or "value". >> >>>> >> >>>> The examples are great though. >> >>>> >> >>>> Best, >> >>>> Kasper >> >>>> >> >>>> [[alternative HTML version deleted]] >> >>> >> >>> ______________________________**_________________ >> >>> Bioconductor mailing list >> >>> Bioconductor at r-project.org >> >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >>> Search the archives: http://news.gmane.org/gmane.** >> >>> science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >>> >> >> >> >> ______________________________**_________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >> Search the archives: http://news.gmane.org/gmane.** >> >> science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> > >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k
On Fri, Aug 2, 2013 at 10:46 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Thu, Aug 1, 2013 at 7:39 PM, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> and, continuing on this important new resource, shouldn't the following >> work? >> >>> class(x) >> [1] "AnnotationHub" >> attr(,"package") >> [1] "AnnotationHub" >>> x >> class: AnnotationHub >> length: 7855 >> filters: none >> hubUrl: http://annotationhub.bioconductor.org/ah >> snapshotVersion: 2.13; snapshotDate: 2013-06-26 >> hubCache: /Users/stvjc/.AnnotationHub >>> keys(x, keytype="Description") >> >> Enter a frame number, or 0 to exit >> >> 1: keys(x, keytype = "Description") >> 2: keys(x, keytype = "Description") >> 3: .local(x, keytype, ...) >> 4: .keys(snapshotUrl(x), keytype) >> 5: unique(.parseJSON(url)) >> 6: .parseJSON(url) >> 7: tryCatch({ >> tmp <- tempfile() >> if (getOption("AnnotationHub.debug", FAL >> 8: tryCatchList(expr, classes, parentenv, handlers) >> 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) >> 10: value[[3]](cond) >> > > > This is fixed now. I should have mentioned that the problem was fixed on the server side, so you don't need to download the latest AnnotationHub, it should "just work" now. Dan > Thanks. > Dan > > >> i'd also suggest that ahinfo() return an object, not end with a message. >> >>> sessionInfo() >> R version 3.0.1 Patched (2013-06-02 r62857) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] >> en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII >> >> attached base packages: >> [1] parallel stats graphics grDevices datasets utils tools >> [8] methods base >> >> other attached packages: >> [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 >> [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 >> [7] digest_0.6.3 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 >> [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 >> [7] stats4_3.0.1 XVector_0.1.0 >> >> >> >> On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen < >> kasperdanielhansen at gmail.com> wrote: >> >>> Hijacking the thread to discuss TAB completion as well. >>> >>> hub = AnnotationHub() >>> hub$<tab> >>> # looks good, let me try goldenpath >>> hub$goldenpath.<tab> >>> hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] >>> hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] >>> hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] >>> hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] >>> hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] >>> hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] >>> hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] >>> hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] >>> hub$goldenpath.vicPac1.database. ... [14] >>> hub$goldenpath.xenTro ... [34] >>> >>> This is a bit useless, since mostly I see single letters. I would suggest >>> the following >>> >>> First, the names tend to be super long. So don't start the examples with >>> the entire path, like >>> hub$goldenpath.a >>> but perhaps something like >>> "current selection: goldenpath. >>> a.. [59] >>> b.. [110] >>> etc, so that goldenpath is only listed once. That way, the suggestions are >>> shorter and it is clearer what the choices are between (at least I think >>> that is the case) >>> >>> Now, when I go down the list to >>> hub$goldenpath.hg19.encodeDCC.wgEncode >>> >>> I get >>> >>> Possible completions are: >>> hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroadHi stone ... >>> [280] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAff yExon ... >>> [107] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode ... [4] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage ... [108] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] >>> >>> But for example, for wgEncodeA, it turns out that there are only two real >>> choices: >>> hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip ... >>> [52] >>> hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase ... >>> [124] >>> >>> but I can't really see this. >>> >>> Anyway, I know this is hard to program, but right now it is a bit hard to >>> explore using the TAB completion. Perhaps this can all be fixed by having >>> more suggestions (there is probably a limited to how many suggestions to >>> show). In this particular case, with this many choices of resources, I >>> guess I would rather have (many) more suggestions than fewer. >>> >>> At the end I just did >>> print(names(hub)) >>> and looked at that, which is probably not what we want. >>> >>> Best, >>> Kasper >>> >>> >>> >>> On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < >>> kasperdanielhansen at gmail.com> wrote: >>> >>> > Technically yes, since I can do >>> > >>> > function(path) { >>> > [[(hub, path) >>> > } >>> > >>> > Still, I think it does make sense to have something a bit more standard >>> (I >>> > find the [[ to be a bit unusual, but that may be colored by how I >>> > program). >>> > >>> > Retrieving multiple resources in a single call, like >>> > paths = names(hub)[1:10] >>> > is going to be used a lot, I predict. >>> > >>> > Kasper >>> > >>> > >>> > >>> > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >>> > >>> >> Hi Kasper, >>> >> >>> >> I think you could just do the following: >>> >> >>> >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** >>> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] >>> >> >>> >> Instead of using $like usual: >>> >> >>> >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** >>> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData >>> >> >>> >> >>> >> Does that solve your problem? >>> >> >>> >> >>> >> Marc >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: >>> >> >>> >>> I was wrong about ahinfo. Is there an exposed interface to getting the >>> >>> result of a path, assuming the path is a character vector. I see I can >>> >>> do >>> >>> AnnotationHub:::.getResource(**hub, path) >>> >>> with hub an AnnotationHub and path a character vector. >>> >>> >>> >>> Such an interface would be extremely useful. >>> >>> >>> >>> >>> >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < >>> >>> kasperdanielhansen at gmail.com> wrote: >>> >>> >>> >>> About ?AnnotationHub (package version 1.1.8) >>> >>>> >>> >>>> All the functions whose values are described under "Value" are not >>> >>>> described under "Usage". All the functions listed under "Usage" are >>> not >>> >>>> described under "Value". >>> >>>> >>> >>>> The ahinfo (which seems to be a key function for doing things >>> >>>> programmatically) is not described under either "usage" or "value". >>> >>>> >>> >>>> The examples are great though. >>> >>>> >>> >>>> Best, >>> >>>> Kasper >>> >>>> >>> >>>> [[alternative HTML version deleted]] >>> >>> >>> >>> ______________________________**_________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor at r-project.org >>> >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>> >>> Search the archives: http://news.gmane.org/gmane.** >>> >>> science.biology.informatics.**conductor< >>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>> >>> >>> >> >>> >> ______________________________**_________________ >>> >> Bioconductor mailing list >>> >> Bioconductor at r-project.org >>> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>> >> Search the archives: http://news.gmane.org/gmane.** >>> >> science.biology.informatics.**conductor< >>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>> >> >>> > >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k
On 08/01/2013 07:39 PM, Vincent Carey wrote: > and, continuing on this important new resource, shouldn't the > following work? > > > class(x) > [1] "AnnotationHub" > attr(,"package") > [1] "AnnotationHub" > > x > class: AnnotationHub > length: 7855 > filters: none > hubUrl: http://annotationhub.bioconductor.org/ah > snapshotVersion: 2.13; snapshotDate: 2013-06-26 > hubCache: /Users/stvjc/.AnnotationHub > > keys(x, keytype="Description") > > Enter a frame number, or 0 to exit > > 1: keys(x, keytype = "Description") > 2: keys(x, keytype = "Description") > 3: .local(x, keytype, ...) > 4: .keys(snapshotUrl(x), keytype) > 5: unique(.parseJSON(url)) > 6: .parseJSON(url) > 7: tryCatch({ > tmp <- tempfile() > if (getOption("AnnotationHub.debug", FAL > 8: tryCatchList(expr, classes, parentenv, handlers) > 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) > 10: value[[3]](cond) > > i'd also suggest that ahinfo() return an object, not end with a message. > Actually, I added an argument the other day to let it do that, although I don't expect most people will need the argument. So if you want the metadata as a list you can do this: library(AnnotationHub) ah = AnnotationHub() ahinfo(ah, path="goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfS tdPkRep1.narrowPeak_0.0.1.RData", returnMeta=TRUE) And it returns a list object instead of just displaying a pretty message. I am currently using this to automagically add the metadata onto GRanges and GRangesList objects when you ask for them. Marc > > sessionInfo() > R version 3.0.1 Patched (2013-06-02 r62857) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] > en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII > > attached base packages: > [1] parallel stats graphics grDevices datasets utils tools > [8] methods base > > other attached packages: > [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 > [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 > [7] digest_0.6.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 > [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 > [7] stats4_3.0.1 XVector_0.1.0 > > > > On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen > <kasperdanielhansen@gmail.com <mailto:kasperdanielhansen@gmail.com="">> > wrote: > > Hijacking the thread to discuss TAB completion as well. > > hub = AnnotationHub() > hub$<tab> > # looks good, let me try goldenpath > hub$goldenpath.<tab> > hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] > hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] > hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] > hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] > hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] > hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] > hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] > hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] > hub$goldenpath.vicPac1.database. ... [14] > hub$goldenpath.xenTro ... [34] > > This is a bit useless, since mostly I see single letters. I would > suggest > the following > > First, the names tend to be super long. So don't start the > examples with > the entire path, like > hub$goldenpath.a > but perhaps something like > "current selection: goldenpath. > a.. [59] > b.. [110] > etc, so that goldenpath is only listed once. That way, the > suggestions are > shorter and it is clearer what the choices are between (at least I > think > that is the case) > > Now, when I go down the list to > hub$goldenpath.hg19.encodeDCC.wgEncode > > I get > > Possible completions are: > hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] > hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroad Histone > ... > [280] > hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] > hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeA ffyExon > ... > [107] > hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode > ... [4] > hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] > hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] > hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage > ... [108] > hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] > hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] > > But for example, for wgEncodeA, it turns out that there are only > two real > choices: > hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip > ... > [52] > hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase > ... > [124] > > but I can't really see this. > > Anyway, I know this is hard to program, but right now it is a bit > hard to > explore using the TAB completion. Perhaps this can all be fixed > by having > more suggestions (there is probably a limited to how many > suggestions to > show). In this particular case, with this many choices of > resources, I > guess I would rather have (many) more suggestions than fewer. > > At the end I just did > print(names(hub)) > and looked at that, which is probably not what we want. > > Best, > Kasper > > > > On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com > <mailto:kasperdanielhansen@gmail.com>> wrote: > > > Technically yes, since I can do > > > > function(path) { > > [[(hub, path) > > } > > > > Still, I think it does make sense to have something a bit more > standard (I > > find the [[ to be a bit unusual, but that may be colored by how I > > program). > > > > Retrieving multiple resources in a single call, like > > paths = names(hub)[1:10] > > is going to be used a lot, I predict. > > > > Kasper > > > > > > > > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson@fhcrc.org> <mailto:mcarlson@fhcrc.org>> wrote: > > > >> Hi Kasper, > >> > >> I think you could just do the following: > >> > >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] > >> > >> Instead of using $like usual: > >> > >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData > >> > >> > >> Does that solve your problem? > >> > >> > >> Marc > >> > >> > >> > >> > >> > >> > >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: > >> > >>> I was wrong about ahinfo. Is there an exposed interface to > getting the > >>> result of a path, assuming the path is a character vector. I > see I can > >>> do > >>> AnnotationHub:::.getResource(**hub, path) > >>> with hub an AnnotationHub and path a character vector. > >>> > >>> Such an interface would be extremely useful. > >>> > >>> > >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < > >>> kasperdanielhansen@gmail.com > <mailto:kasperdanielhansen@gmail.com>> wrote: > >>> > >>> About ?AnnotationHub (package version 1.1.8) > >>>> > >>>> All the functions whose values are described under "Value" > are not > >>>> described under "Usage". All the functions listed under > "Usage" are not > >>>> described under "Value". > >>>> > >>>> The ahinfo (which seems to be a key function for doing things > >>>> programmatically) is not described under either "usage" or > "value". > >>>> > >>>> The examples are great though. > >>>> > >>>> Best, > >>>> Kasper > >>>> > >>>> [[alternative HTML version deleted]] > >>> > >>> ______________________________**_________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > >>> > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >>> Search the archives: http://news.gmane.org/gmane.** > >>> > science.biology.informatics.**conductor<http: news.gmane.org="" gm="" ane.science.biology.informatics.conductor=""> > >>> > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >> Search the archives: http://news.gmane.org/gmane.** > >> > science.biology.informatics.**conductor<http: news.gmane.org="" gm="" ane.science.biology.informatics.conductor=""> > >> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
0
5.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Thanks Kasper, This has been cleaned up. Marc On 07/31/2013 06:02 PM, Kasper Daniel Hansen wrote: > About ?AnnotationHub (package version 1.1.8) > > All the functions whose values are described under "Value" are not > described under "Usage". All the functions listed under "Usage" are not > described under "Value". > > The ahinfo (which seems to be a key function for doing things > programmatically) is not described under either "usage" or "value". > > The examples are great though. > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor