On Wed, Oct 30, 2013 at 8:37 AM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> > On 10/30/2013 07:55 AM, Michael Lawrence wrote: > >> >> >> >> On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès <hpa...@fhcrc.org >> <mailto:hpa...@fhcrc.org>> wrote: >> >> Hi Michael, >> >> In Bioc < 2.13, subsetting was a mess. In particular, handling of >> list-like subscripts was rather unpredictable. It would work only >> if you were lucky enough to try it with one of the few supported >> types (like IntegerList, LogicalList, or IRangesList), but it didn't >> work for other very natural types like list or CharacterList. >> Or it would work for [ but not for [<-, or vice-versa: >> >> x <- splitAsList(letters[1:6], c(2, 4, 3, 2, 2, 4)) >> x[list(1)] # doesn't work in BioC < 2.13! >> x[list(1)] <- "XX" # works in BioC < 2.13! >> >> Or, if both [ and [<- worked, they could behave inconsistently: one >> would require the list-like subscript to have the same length as 'x' >> but the other wouldn't. Or one would use the names on the subscript >> and on 'x' to map the list elements between the two, but the other >> wouldn't. >> >> Hopefully in BioC 2.13, subsetting behaves more consistently (at least >> that was the intention). For example now the names on the subscript >> and >> on 'x' are always used to map the list elements between the two: >> >> > x[list(`4`=2:1)] >> CharacterList of length 1 >> [["4"]] f b >> >> Also now, it's an error if the subscript has names but 'x' has not: >> >> > unname(x)[list(`4`=2:1)] >> Error in subsetListByList(x, i) : >> >> cannot subscript an unnamed list-like object by a named >> list-like object >> >> (I should probably change this message for: "cannot subset an unnamed >> list-like object by a named list-like subscript".) >> >> This is to be consistent with subsetting a Vector object by name, >> which >> fails if 'x' has no names: >> >> > IRanges(1:4, 5)["a"] >> >> Error in normalizeSingleBracketSubscrip**__t(i, x) : >> cannot subset by character when names are NULL >> >> If the subscript is a list-like object with names, the assumption is >> that the user intended those names to be mapped against 'x' names. >> >> >> >> Why make this assumption? >> > > As I said, this is how [<- was behaving in Bioc < 2.13, but not [. > When reunifying a choice has to be made, and I chose to make [ > behave like [<- and not the other way around. For 3 reasons: > 1. It makes subsetting by a list-like object more flexible. > 2. It feels more consistent with what subsetting a Vector object > by name does. > 3. It's also consistent with what findOverlaps() and > subsetByOverlaps() have been doing for years on named > RangesList objects. > > > Three users here have not made it and were >> surprised by the names on the index having any relevance to extraction. >> > > The good news is that now that they've been surprised by this, they > won't be surprised by the behavior of subsetByOverlaps() ;-) > We cannot totally eliminate user surprises (depends too much on > individual backgrounds), but we can minimize them by providing > consistent behavior. > > A long time ago we decided that the extraction should just happen in parallel, and that subsetByOverlaps on RangesList was a special case (it's already so different from basic [ extraction). Apparently, we forgot to take out the [<- stuff. So I would argue that the change should go the other way. Users will not expect the name-based matching. At least that was the consensus 4 years ago. Others should chime on in this discussion. Should List-wise extraction and replacement match by the names of the List elements? H. > > > >> If 'x' doesn't have names, I think it should fail rather than silently >> fall back to position-based mapping. So at least you give a chance >> to the user to either put names on 'x' (maybe s/he just forgot) or to >> remove them from the subscript. If we really want to fall back to >> position-based mapping, at least it should issue a warning, I think. >> >> One thing I didn't change from pre-BioC-2.13 behavior is that a >> list-like subscript (when unnamed) is not recycled along 'x'. It's >> open to discussion whether this would be a good thing to have or not. >> Changing this would be pretty disruptive though... >> >> Cheers, >> H. >> >> >> >> On 10/29/2013 03:51 PM, Michael Lawrence wrote: >> >> I think we should just drop the names for the user. The Bioc <2.13 >> behavior seems reasonable to me. Please elaborate on the subtle >> issues. >> Most users would not expect the *names* on the index to have any >> effect >> on the extraction, in accordance with the behavior of ordinary >> vectors. >> The only difference with Lists is that there is a partitioning, >> which >> seems unrelated to naming. >> >> Michael >> >> >> On Tue, Oct 29, 2013 at 3:40 PM, Hervé Pagès <hpa...@fhcrc.org >> <mailto:hpa...@fhcrc.org> >> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>>> wrote: >> >> Hi Thomas, >> >> For the same reasons that you cannot subset by names a >> Vector object >> with no names: >> >> > IRanges(1:4, width=10)[letters[1:4]] >> Error in normalizeSingleBracketSubscrip**____t(i, x) : >> >> >> cannot subset by character when names are NULL >> >> you cannot subset an unnamed List object using a named >> list-like >> subscript. So in your case, just remove the names on >> 'keep_ranges' >> (which are probably not desired anyway) before using it as a >> subscript: >> >> >> > keep_ranges >> CompressedIRangesList of length 18 >> $`1` >> IRanges of length 1 >> start end width >> [1] 20 108 89 >> >> $`2` >> IRanges of length 1 >> start end width >> [1] 43 131 89 >> >> $`3` >> IRanges of length 1 >> start end width >> [1] 21 105 85 >> >> ... >> <15 more elements> >> >> > return_rles[ unname(keep_ranges) ] >> RleList of length 18 >> [[1]] >> logical-Rle of length 89 with 1 run >> Lengths: 89 >> Values : TRUE >> >> [[2]] >> logical-Rle of length 89 with 1 run >> Lengths: 89 >> Values : TRUE >> >> [[3]] >> logical-Rle of length 85 with 1 run >> Lengths: 85 >> Values : TRUE >> >> [[4]] >> logical-Rle of length 85 with 1 run >> Lengths: 85 >> Values : TRUE >> >> [[5]] >> logical-Rle of length 102 with 1 run >> Lengths: 102 >> Values : TRUE >> >> ... >> <13 more elements> >> >> Prior to BioC 2.13, it was possible to subset an unnamed >> List object by >> a named list-like subscript, and in that case, the names on >> the >> subscript were ignored and the subscript was treated as >> parallel to the >> object to subset. However this behavior was somehow >> dangerous (could >> lead to subtle issues) and didn't follow the spirit of what >> subsetting >> an unnamed Vector by name does. So it's not supported >> anymore. >> >> Sorry for the inconvenience, >> H. >> >> >> >> On 10/29/2013 03:05 PM, Thomas Sandmann wrote: >> >> Hi Herve, >> >> I have updated to IRanges 1.20.4 now, but >> unfortunately, I still >> encounter an error when I try to subset a >> CompressedRleList or >> SimpleRleList with a CompressedIRangesList or >> SimpleIRangesList. >> >> Would you mind having a look at where I am going wrong >> ? (My two >> example >> objects are available in the rdata object at the url >> shown below). >> >> >> con=url("http://dl.__dropboxus**__ercontent.com/u/__126180/__** >> example.rdata<http://dropboxus__ercontent.com/u/__126180/__example.rdata> >> >> <http://dropboxusercontent.**com/u/__126180/example.rdata<http://dropboxusercontent.com/u/__126180/example.rdata> >> > >> >> >> <http://dl.dropboxusercontent.**__com/u/126180/example.rdata >> >> >> <http://dl.dropboxusercontent.**com/u/126180/example.rdata<http://dl.dropboxusercontent.com/u/126180/example.rdata> >> >>") >> load( con ) >> return_rles[ keep_ranges ] >> >> Error in subsetListByList(x, i) (from List-class.R#205) : >> cannot subscript an unnamed list-like object by a >> named >> list-like object >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils >> datasets >> methods >> [8] base >> >> other attached packages: >> [1] trimPrimers_1.3.0 Rsamtools_1.14.1 >> Biostrings_2.30.0 >> [4] GenomicRanges_1.14.2 XVector_0.2.0 >> IRanges_1.20.4 >> [7] BiocGenerics_0.8.0 Defaults_1.1-1 >> BiocInstaller_1.12.0 >> [10] roxygen2_2.2.2 digest_0.6.3 >> devtools_1.3 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-6 brew_1.0-6 compiler_3.0.2 >> evaluate_0.5.1 httr_0.2 >> [6] memoise_0.1 RCurl_1.95-4.1 stats4_3.0.2 >> stringr_0.6.2 >> tools_3.0.2 >> [11] whisker_0.3-2 zlibbioc_1.8.0 >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> >> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> <tel:%28206%29%20667-1319> >> >> ______________________________**_____________________ >> Bioc-devel@r-project.org >> <mailto:Bioc-devel@r-project.**org<Bioc-devel@r-project.org> >> > >> <mailto:Bioc-devel@r-project._**_org >> <mailto:Bioc-devel@r-project.**org <Bioc-devel@r-project.org>>> >> mailing list >> >> https://stat.ethz.ch/mailman/_**___listinfo/bioc-devel<https://stat.ethz.ch/mailman/____listinfo/bioc-devel> >> >> <https://stat.ethz.ch/mailman/**__listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel> >> > >> >> >> <https://stat.ethz.ch/mailman/**__listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel> >> >> <https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]
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