Vince, Michael,
 
Thanks both of you. It is good to know that the devel version works correctly. I guess it is always a good idea to get the most recent devel version. 

Have a great weekend!

Xiwei

________________________________

From: Michael Lawrence [mailto:lawrence.michael@gene.com]
Sent: Sat 1/30/2010 8:38 PM
To: Vincent Carey
Cc: Wu, Xiwei; Michael Lawrence; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] FindOverlaps Problem




On Sat, Jan 30, 2010 at 1:33 PM, Vincent Carey <stvjc@channing.harvard.edu> wrote:


	ah -- my result was with devel, and in fact it does not agree with
	yours, but it seems correct in this instance.
	
	


I think there was a bug in the as.matrix() method on the overlap result that was fixed relatively recently. This probably explains the difference.

Thanks for looking into this Vince.

Michael



	> sessionInfo()
	R version 2.11.0 Under development (unstable) (2010-01-07 r50940)
	i386-apple-darwin9.8.0
	
	locale:
	[1] C
	
	attached base packages:
	[1] grid      stats     graphics  grDevices datasets  tools     utils
	[8] methods   base
	
	other attached packages:
	 [1] GenomeGraphs_1.7.1  biomaRt_2.3.0       leeBamSet_0.0.8
	 [4] Rsamtools_0.1.24    BSgenome_1.15.4     Biostrings_2.15.18
	 [7] IRanges_1.5.31      org.Sc.sgd.db_2.3.5 RSQLite_0.7-3
	[10] DBI_0.2-4           AnnotationDbi_1.9.0 Biobase_2.7.0
	[13] weaver_1.13.0       codetools_0.2-2     digest_0.4.1
	

	loaded via a namespace (and not attached):
	
	[1] RCurl_1.3-0 XML_2.6-0
	


	On Sat, Jan 30, 2010 at 4:30 PM, Vincent Carey
	<stvjc@channing.harvard.edu> wrote:
	> 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@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@gene.com]
	>> Sent: Friday, January 29, 2010 1:13 PM
	>> To: Wu, Xiwei
	>> Cc: bioconductor@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@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
	>>
	>>
	>> ---------------------------------------------------------------------
	>> SECURITY/CONFIDENTIALITY WARNING:  \ This message and ...{{dropped:10}}
	>>
	>> _______________________________________________
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	>>
	>
	



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