[BioC] function precede() not working with GRanges

[Martin Morgan]

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

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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