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 <nat...@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@queryHits
Using queryHits(fo) works, and using fo@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
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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
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E-mail: hpa...@fredhutch.org
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Fax: (206) 667-1319
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