[Bioc-devel] IRanges findOverlaps and queryHits

Thu Dec 29 08:59:11 CET 2016

A couple more things about this: The Hits class is defined in the
S4Vectors package. The changes to the internals of the class happened
in BioC 3.3, almost 1 year ago. The NEWS file in S4Vectors has an entry
under "CHANGES IN VERSION 0.10.0" that describes these changes:

     o Many changes to the Hits class:
       - Replace the old Hits class (where the hits had to be sorted by 
query)
         with the SortedByQueryHits class.
       - A new Hits class where the hits can be in any order is 
re-introduced as
         the parent of the SortedByQueryHits class.
       - The Hits() constructor gets the new 'sort.by.query' argument 
that is
         FALSE by default. When 'sort.by.query' is set to TRUE, the 
constructor
         returns a SortedByQueryHits instance instead of a Hits instance.
       - Bidirectional coercion is supported between Hits and 
SortedByQueryHits.
         When going from Hits to SortedByQueryHits, the hits are sorted 
by query.
       - Add "c" method for Hits objects.
       - Rename Hits slots:
           queryHits -> from
           subjectHits -> to
           queryLength -> nLnode (nb of left nodes)
           subjectLength -> nRnode (nb of right nodes)
       - Add updateObject() method to update serialized Hits objects 
from old
         (queryHits/subjectHits) to new (from/to) internal representation.
       - The "show" method for Hits objects now labels columns with 
from/to by
         default and switches to queryHits/subjectHits labels only when the
         object is a SortedByQueryHits object.
       - New accessors are provided that match the new slot names: 
from(), to(),
         nLnode(), nRnode(). The old accessors (queryHits(), subjectHits(),
         queryLength(), and subjectLength()) are just aliases for the new
         accessors. Also countQueryHits() and countSubjectHits() are now 
aliases
         for new countLnodeHits() and countRnodeHits().

Hope this helps,

H.

On 12/20/2016 12:43 PM, Michael Lawrence wrote:
> Hi Nathan,
>
> Direct slot access is strongly discouraged, for this very reason. Please
> stick to using the accessor.
>
> And yes, Hits was redefined in terms of a graph model last devel cycle.
>
> Michael
>
> On Tue, Dec 20, 2016 at 12:16 PM, Nathan Sheffield <nathan at code.databio.org>
> wrote:
>
>> Did the findOverlaps return object get a @queryHits slot removed recently?
>>
>> I recently got this error running some of my code:
>>
>> Error: no slot of name "queryHits" for this object of class
>> "SortedByQueryHits"
>>
>> My workflow is basically,
>>
>> fo = findOverlaps(...)
>> fo at queryHits
>>
>> Using queryHits(fo) works, and using fo at queryHits to access it via slot
>> has always worked for me as well -- until this time. I couldn't find
>> anything in a changelog describing any changes into IRanges slots. Thought
>> someone here might be able to shed some light on that for me... does anyone
>> know what happened to the ability to access with @queryHits? Some relevant
>> sessionInfo():
>>
>>> sessionInfo()
>> R version 3.3.0 (2016-05-03)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS release 6.8 (Final)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C 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
>> LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
>> methods   base
>>
>> other attached packages:
>>  [1] RGenomeUtils_0.01 BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99
>> BSgenome.Hsapiens.UCSC.hg19_1.4.0
>>  [4] BSgenome_1.42.0 rtracklayer_1.34.1 Biostrings_2.42.0
>>  [7] XVector_0.14.0 LOLA_1.4.0 GenomicRanges_1.26.1
>> [10] GenomeInfoDb_1.10.1 IRanges_2.8.1 S4Vectors_0.12.0
>> [13] BiocGenerics_0.20.0 ggplot2_2.1.0 simpleCache_0.0.1
>> [16] extrafont_0.17 data.table_1.9.6 devtools_1.12.0
>> [19] project.init_0.0.1
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.7                plyr_1.8.4 bitops_1.0-6
>>  tools_3.3.0
>>  [5] zlibbioc_1.20.0            testthat_1.0.2 digest_0.6.10
>> lattice_0.20-33
>>  [9] memoise_1.0.0              gtable_0.2.0 Matrix_1.2-6
>>  yaml_2.1.13
>> [13] Rttf2pt1_1.3.4             withr_1.0.2 stringr_1.1.0
>> roxygen2_5.0.1
>> [17] grid_3.3.0                 Biobase_2.34.0 R6_2.2.0
>>  BiocParallel_1.8.1
>> [21] XML_3.98-1.4               reshape2_1.4.2 extrafontdb_1.0
>> magrittr_1.5
>> [25] GenomicAlignments_1.10.0   Rsamtools_1.26.1 scales_0.4.1
>>  SummarizedExperiment_1.4.0
>> [29] colorspace_1.3-0           stringi_1.1.2 RCurl_1.95-4.8
>>  munsell_0.4.3
>> [33] chron_2.3-47               crayon_1.3.2
>>>
>>
>>
>> -Nathan
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
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