[BioC] FindOverlaps Problem

[Wu, Xiwei]

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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