[BioC] function precede() not working with GRanges

[Martin Morgan]

On 01/04/2011 01:15 PM, Michael Lawrence wrote:
> 
> 
> On Tue, Jan 4, 2011 at 11:52 AM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
> 
>     On 01/04/2011 11:34 AM, Jeremiah Degenhardt wrote:
>     > Hello Bioconductor,
>     >
>     > I am trying to use the function precede() with two GRanges objects
>     to find
>     > the closest element from gr1 to an element in gr2. precede() shows
>     that it
>     > should work with a GRanges object, however, when I try to use it
>     it returns
>     > only a vector of "NA".
>     >
>     > Pasted below is a simplified bit of code to reproduce the error and my
>     > session info.
>     >
>     > Additionally, it would be even nicer if the function nearest() were
>     > implemented for a GRanges object.
>     >
>     > Thanks in advance for the help
> 
>     Hi Jeremiah --
> 
>     Provide strand information for at least one of the reads, e.g.,
> 
>     > gr1 <- GRanges("chr1", IRanges(1,10), "-")
>     > gr2 <- GRanges("chr1", IRanges(20,30))
>     > precede(gr2, gr1)
>     [1] 1
> 
>     or do the comparison on IRanges with
> 
>     > precede(ranges(gr1), ranges(gr2))
>     [1] 1
> 
> 
> This does not work in general, because it discards the chromosome.
> GRanges is often treated as a flat RangesList/RangedData, with the
> strand set to "*".
> 
> Jeremiah and I think it would be reasonable to treat a '*' range as a
> '+' range when comparing to another '*' range. That is, assume strand is
> unknown/irrelevant and just go by the starts and ends as if it were a
> Ranges object, except considering the sequence.

Was wondering about use case details, e.g., are all query & subject '*'?
Martin

> Obviously, one could often just explicitly coerce the strand to '+', but
> the user is not going to expect that such a coercion is required.
> Especially people like us who are too lazy to figure out how to find the
> documentation on an S4 method.
> 
> Michael
> 
>     nearest will be implemented.
> 
>     Martin
> 
>     > Jeremiah
>     >
>     >> gr1 <- GRanges("chr1", IRanges(1,10))
>     >> gr2<- GRanges("chr1", IRanges(20,30))
>     >> precede(gr2, gr1)
>     > [1] NA
>     >>
>     >
>     >> sessionInfo()
>     > R version 2.13.0 Under development (unstable) (2010-12-07 r53809)
>     > Platform: x86_64-unknown-linux-gnu (64-bit)
>     >
>     > 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=en_US.UTF-8
>     >  [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] grid      stats     graphics  grDevices utils     datasets
>      methods
>     > [8] base
>     >
>     > other attached packages:
>     >  [1] motifRG_0.0.2       rtracklayer_1.11.8  RCurl_1.5-0
>     >  [4] bitops_1.0-4.1      seqLogo_1.17.0      chipseq_1.1.2
>     >  [7] ShortRead_1.9.8     Rsamtools_1.3.11    lattice_0.18-3
>     > [10] BSgenome_1.19.2     Biostrings_2.19.2   GenomicRanges_1.3.5
>     > [13] IRanges_1.9.16      multicore_0.1-3
>     >
>     > loaded via a namespace (and not attached):
>     > [1] Biobase_2.11.6 hwriter_1.3    tools_2.13.0   XML_3.2-0
>     >
>     >       [[alternative HTML version deleted]]
>     >
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> 
>     --
>     Computational Biology
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
>     Location: M1-B861
>     Telephone: 206 667-2793
> 
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-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793