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

[Steve Lianoglou]

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