Hi Peter,
On 05/26/2014 04:37 PM, Peter Hickey wrote:
Thanks for the suggested work-around, Martin. In order to define the method on the group
generic 'Ops' rather than '==' I will need to generalise .MTuples.compare to the 'Arith',
'Compare' and 'Logic' sub-groups listed in ?Ops, won't I? I'll try to implement the
comparison methods for MTuples via the 'Ops' group generic but I want to first make sure
that I'm not missing out on getting some of these "for free". The rest of this
post might be tangential to the issue I first raised, but it also explains why I
implemented '==' rather than on the group generic 'Ops'.
The MTuples class extends GRanges:
setClass('MTuples', representation(extraPos = "matrix"), contains = "GRanges",
validity = .valid.MTuples)
I defined .MTuples.compare because while MTuples is based on GRanges, the GRanges 'compare' method is
inappropriate for MTuples (see
https://github.com/PeteHaitch/cometh/blob/8be01b8b37b6288db5493f53188a193a423ab69f/R/methods-MTuples-class.R
if interested). Based on reading ?compare, I'd hoped that the binary "parallel" comparison
operators (<=, ==, !=, >=, < and >) would work out-of-the-box. But I already found that I
needed to include explicit method definitions for '<=' and '==' because otherwise these (and the other
binary comparison operators) would dispatch on the GRanges methods rather than the MTuples methods. This is
because the GRanges '==' and '<=' methods are explicitly implemented as:
setMethod("==", signature(e1="GenomicRanges", e2="GenomicRanges"), function(e1,
e2) { .GenomicRanges.compare(e1, e2) == 0L })
setMethod("<=", signature(e1="GenomicRanges", e2="GenomicRanges"), function(e1,
e2) { .GenomicRanges.compare(e1, e2) <= 0L })
I don't understand why these explicit definitions are necessary; the 'compare'
method for GRanges is already defined so why don't these work out-of-the-box,
which is what I expected based on my reading of ?compare (specifically, point 1
in the Note sub-section).
You're right, they are not needed. I just removed them from
GenomicRanges 1.17.17. See if that helps with the original problem
you reported.
Cheers,
H.
Because these are explicitly defined, and not simply defined via inheritance, I must also
explicitly define '<=' and '==' methods for MTuples (although I do get '>=', '!=',
'<' and '>' for free, which is great!). Unfortunately, as you can see, the MTuples
'==' method breaks '==' for other signatures. Hope that wasn't too tangential.
Cheers,
Pete
On 27/05/2014, at 2:44 AM, Martin Morgan <mtmor...@fhcrc.org> wrote:
On 05/25/2014 09:39 PM, Peter Hickey wrote:
The "==" method that I have defined for my class, MTuples, is breaking the "==" method for signature
c("Rle", "vector"). I discovered this when working on something quite unrelated, namely, I couldn't resize
IRanges with "fixed = end" when my package was loaded. The attached code highlights the initial problem.
The error message and traceback were a little hairy - could someone please help
me figure out what's going wrong?
I don't have an immediate answer. A work-around is to define the method on the
group generic 'Ops' rather than '==', though maybe the generalization of
.MTuples.compare to other members of the Ops family is not easy?
setMethod("Ops", c("MTuples", "MTuples"), function(e1, e2) TRUE)
Martin
Thanks,
Pete
------------------------------------------------------------------------------------------------------------------
# Mimics the initial problem
# Fresh R session
library(IRanges)
ir <- IRanges(start = 11, end = rep.int(20, 5))
# Works when repeatedly called
resize(ir, 1, 'end') # Works
resize(ir, 1, 'end') # Works
# The method definition that breaks things
# I haven't included the MTuples class definition or the .MTuples.compare
function
# But that shouldn't matter in order to highlight the problem, should it?
setMethod("==", c("MTuples", "MTuples"), function(e1, e2) {
.MTuples.compare(e1, e2) == 0L
})
# No longer works
resize(ir, 1, 'end')
------------------------------------------------------------------------------------------------------------------
I managed to simplify the reproducible example to the following, but I can't
figure out what's going wrong:
------------------------------------------------------------------------------------------------------------------
# A simplified example
# Fresh R session
library(IRanges)
fix <- Rle('end', 10)
# Works when repeatedly called
fix == 'end' # Works
fix == 'end' # Works
# The method definition that breaks things
# I haven't included the MTuples class definition or the .MTuples.compare
function
# But that shouldn't matter in order to highlight the problem, should it?
setMethod("==", c("MTuples", "MTuples"), function(e1, e2) {
.MTuples.compare(e1, e2) == 0L
})
# Works the first time, but not the second
fix == 'end' # Works
fix == 'end' # Breaks
------------------------------------------------------------------------------------------------------------------
The same problem occurs if the vector is numeric and not character, e.g. using
7 instead of 'end'.
When this breaks I get the error:
------------------------------------------------------------------------------------------------------------------
Error in Rle(values = callGeneric(runValue(e1)[which1], runValue(e2)[which2]),
:
error in evaluating the argument 'values' in selecting a method for function
'Rle': Error in as.character(call[[1L]]) :
cannot coerce type 'builtin' to vector of type 'character'
------------------------------------------------------------------------------------------------------------------
My session info is:
------------------------------------------------------------------------------------------------------------------
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] IRanges_1.22.7 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] stats4_3.1.0
------------------------------------------------------------------------------------------------------------------
--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
hic...@wehi.edu.au
http://www.wehi.edu.au
______________________________________________________________________
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--
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
hic...@wehi.edu.au
http://www.wehi.edu.au
______________________________________________________________________
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