[BioC] FindOverlaps Problem

[Vincent Carey]

It seems to me that it is working correctly but you can't assume that
the order of ranges at time of construction serves as the order in the
ultimate object.  A lexicographic ordering by space names is used.
Challenging to interpret but if you look at the values of a and b
before interpreting your findOverlaps result it starts to make sense.

> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3,
7), sep=""))
> a
RangedData with 7 rows and 0 value columns across 7 spaces
        space    ranges |
  <character> <IRanges> |
1       chr10   [1, 10] |
2        chr2   [1, 10] |
3        chr3   [1, 10] |
4        chr5   [1, 10] |
5        chr6   [1, 10] |
6        chr7   [1, 10] |
7        chr9   [1, 10] |
> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3
, "X"), sep=""))
> b
RangedData with 7 rows and 0 value columns across 7 spaces
        space    ranges |
  <character> <IRanges> |
1       chr10   [1, 10] |
2       chr18   [1, 10] |
3        chr2   [1, 10] |
4       chr21   [1, 10] |
5        chr3   [1, 10] |
6        chr5   [1, 10] |
7        chrX   [1, 10] |
> findOverlaps(a,b)
RangesMatchingList of length 7
names(7): chr10 chr2 chr3 chr5 chr6 chr7 chr9
> as.matrix(.Last.value)
     query subject
[1,]     1       1
[2,]     2       3
[3,]     3       5
[4,]     4       6


On Sat, Jan 30, 2010 at 1:09 PM, Wu, Xiwei <XWu at coh.org> wrote:
> Michael,
>
> Here is one example. Please let me know if I have missed anything. Thanks.
>
>> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep=""))
>> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep=""))
>> as.matrix(findOverlaps(a, a))
>     query subject
> [1,]     1       1
> [2,]     2       2
> [3,]     3       3
> [4,]     4       4
> [5,]     5       5
> [6,]     6       6
> [7,]     7       7
>> as.matrix(findOverlaps(a, b))
>     query subject
> [1,]     1       1
> [2,]     2       3
> [3,]     3       5
> [4,]     4       5
>> a[4]
> RangedData with 1 row and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1        chr5   [1, 10] |
>> b[5]
> RangedData with 1 row and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1        chr3   [1, 10] |
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=C
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.6.0                  RCurl_1.3-1
> [3] bitops_1.0-4.1                     BSgenome.Hsapiens.UCSC.hg18_1.3.15
> [5] ShortRead_1.4.0                    lattice_0.17-26
> [7] BSgenome_1.14.0                    Biostrings_2.14.0
> [9] IRanges_1.4.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.0 grid_2.10.0   hwriter_1.1   tools_2.10.0  XML_2.6-0
>
>
> Xiwei
> ________________________________________
> From: Michael Lawrence [mailto:lawrence.michael at gene.com]
> Sent: Friday, January 29, 2010 1:13 PM
> To: Wu, Xiwei
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] FindOverlaps Problem
>
> Need input... what is the expected result? and what actually happened? sessionInfo()...
> On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <XWu at coh.org> wrote:
> Dear all,
>
> I found that the findOverlaps function does not work properly if the
> space levels do not match exactly between subject and query. Has anyone
> noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is
> this problem being fixed in the developmental version?
>
> Thanks.
>
> Xiwei
>
>
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