[BioC] IRanges : Strange behavior subsetting an IntervalTree with an indexing variable from within a function

[Martin Morgan]

Hi Steve -- I suspect the developer will get to this shortly, and that
this has to do with internal issues in R. So your best bet is to give it
a break for a couple of hours.

In the mean time, you can find out what's going on with

> selectMethod("[", "IntervalTree")
Method Definition:

function (x, i, j, ..., drop = TRUE)
{
    cl <- class(x)
    mc <- match.call()
    mc$x <- as(x, "IRanges")
    as(eval(mc), cl)
}
<environment: namespace:IRanges>

Signatures:
        x              i     j
target  "IntervalTree" "ANY" "ANY"
defined "Ranges"       "ANY" "ANY"
> trace("[", signature="IntervalTree", tracer=browser)
Tracing specified method for function "[" in package "base"
[1] "["
>        query <- IRanges(c(1, 4, 9), c(5, 7, 10))
>        subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
>        tree <- IntervalTree(subject)
> tree[1:2]
Tracing tree[1:2] on entry
Called from: eval(expr, envir, enclos)
Browse[1]> n

my guess is that 'eval' is in the wrong frame, probably because of the
way the methods package manipulates things. I'm not sure why
"[",IntervalTree was implemented this way.

Martin

Steve Lianoglou wrote:
> Argh!
> 
> Wrapping into the for loop actually didn't fix anything -- the symptoms
> of the problem have matured in a way that make even less sense to me now.
> 
> It just seems as if the value of my indexing variable (``hits``) is
> stuck on the value that was first used when trying to index into my
> IntervalTree -- every time I use ``hits`` it always returns the same
> bunch of Intervals that were returned the first time my interval tree
> was indexed, even though its (hits) current value is different.
> 
> For instance, in the 6th iteration of the loop:
> 
> Browse[1]> hits
>  [1] 3025 3026 3027 3028 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103
> 
> Browse[1]> ir[hits]
> IntervalTree instance:
>     start   end width
> [1] 34576 34581     6
> [2] 34608 34613     6
> [3] 34635 34640     6
> [4] 34888 34893     6
> 
> Clearly that's wrong there should be 13 intervals returned.
> 
> Those values being returned are from the "hits" vector that was
> calculated on the first pass of the loop, which was 158:161. This was
> calc'd 5 iterations ago, though, and should be long since gone!.
> 
> Browse[1]> ir[158:161]
> IntervalTree instance:
>     start   end width
> [1] 34576 34581     6
> [2] 34608 34613     6
> [3] 34635 34640     6
> [4] 34888 34893     6
> 
> Let's make ``hits`` something completely inane:
> 
> Browse[1]> hits <- 0
> Browse[1]> ir[hits]
> IntervalTree instance:
>     start   end width
> [1] 34576 34581     6
> [2] 34608 34613     6
> [3] 34635 34640     6
> [4] 34888 34893     6
> 
> Meh ... this is only happening when indexing my IntervalTree, though:
> 
> Browse[1]> m <- matrix(1:100, 10,10)
> Browse[1]> m[hits]
> integer(0)
> 
> 
> Still -- indexing with a NEW var, one that was never defined before,
> fails again on the IntervalTree:
> 
> Browse[1]> yy <- 1:10
> Browse[1]> ir[yy]
> Error in eval(expr, envir, enclos) : object 'yy' not found
> 
> Browse[1]> m[yy]
> [1]  1  2  3  4  5  6  7  8  9 10
> 
> I'm stuck in bizarro land, and don't know how to get out ... anybody
> have a map?
> 
> -steve
> 
> On Sep 9, 2009, at 1:03 PM, Steve Lianoglou wrote:
> 
>> Hmm ... continuing from the previous email, switching the code out of
>> lapply and into a for loop seems to fix.
>>
>> So, instead of:
>>
>> dist <- lapply(range.list, function(rl) {
>> hits <- subjectHits(overlap(ir, rl))
>> browser() # The debug calls below start from here
>> if (length(hits) > 1) {
>>   diff(start(ir[hits]))
>> } else {
>>   NA
>> }
>> })
>>
>> do this:
>>
>> dist <- list()
>> for (idx in seq(range.list)) {
>>  hits <- subjectHits(overlap(ir, range.list[[idx]]))
>>  dist[[idx]] <- if (length(hits) > 1) {
>>    diff(start(ir[hits]))
>>  } else {
>>    NA
>>  }
>> }
>>
>> That works. Weird, no?
>>
>> Of course, I forgot to mention sessionInfo() -- sorry.
>>
>> R> > sessionInfo()
>> R version 2.10.0 Under development (unstable) (2009-09-07 r49613)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] RSQLite_0.7-2      DBI_0.2-4          ShortRead_1.3.33  
>> lattice_0.17-25    BSgenome_1.13.11   doMC_1.1.1         multicore_0.1-3
>> [8] foreach_1.2.1      codetools_0.2-2    iterators_1.0.2   
>> Biostrings_2.13.36 IRanges_1.3.69     ARE.utils_0.1.0
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.5.5 grid_2.10.0   hwriter_1.1   tools_2.10.0
>>
>> -steve
>>
>> -- 
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  |  Memorial Sloan-Kettering Cancer Center
>>  |  Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
> 
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