[Bioc-sig-seq] reduce error on RangedData with unused space names

[Ivan Gregoretti]

Hi Michael and Janet,

I think that the reduce bug still persists in the devel branch. I
updated all my Bioconductor packages yesterday and yet, following her
steps I get

> reduce(myregions_RD)
Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism

I hope the sessionInfo() helps.

Thank you,

Ivan

> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-12-02 r53747)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ChIPpeakAnno_1.7.0                  limma_3.7.23
 [3] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
 [5] RSQLite_0.9-4                       DBI_0.2-5
 [7] AnnotationDbi_1.13.13               BSgenome.Ecoli.NCBI.20080805_1.3.17
 [9] multtest_2.7.1                      Biobase_2.11.8
[11] biomaRt_2.7.1                       BSgenome.Mmusculus.UCSC.mm9_1.3.17
[13] BSgenome_1.19.3                     Biostrings_2.19.9
[15] GenomicRanges_1.3.18                IRanges_1.9.22

loaded via a namespace (and not attached):
[1] MASS_7.3-11     RCurl_1.5-0     splines_2.13.0  survival_2.36-5
[5] XML_3.2-0


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878



On Thu, Feb 24, 2011 at 9:46 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> Thanks. Seems to be fixed already in devel.
>
> On Wed, Feb 23, 2011 at 12:15 PM, Janet Young <jayoung at fhcrc.org> wrote:
>
>> Hi again,
>>
>> I noticed that "reduce" gives an error on RangedData objects if there are
>> space names that contain no ranges:
>>        Error in endoapply(x[, by], FUN) : 'FUN' did not produce an
>> endomorphism
>>
>> I can work around it, but it'd great not to need to do that.  All the
>> details are below.
>>
>> thanks very much,
>>
>> Janet
>>
>> -------------------------------------------------------------------
>>
>> Dr. Janet Young (Trask lab)
>>
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Avenue N., C3-168,
>> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>>
>> tel: (206) 667 1471 fax: (206) 667 6524
>> email: jayoung  ...at...  fhcrc.org
>>
>> http://www.fhcrc.org/labs/trask/
>>
>> -------------------------------------------------------------------
>>
>>
>>
>> > library(IRanges,warn.conflicts=F)
>>
>> > myregions_RD <-
>> RangedData(IRanges(start=c(101L,201L,101L,101L),end=c(250L,300L,220L,501L)),space=c("chr1","chr1","chr1","chr2"),strand=c("+","+","+","+")
>>   )
>>
>> > #### this works
>> > reduce(myregions_RD)
>> RangedData with 2 rows and 1 value column across 2 spaces
>>        space     ranges |      strand
>>  <character>  <IRanges> | <character>
>> 1        chr1 [101, 300] |           +
>> 2        chr2 [101, 501] |           +
>>
>> > ### drop regions that are bigger than 300bp (now there's nothing left on
>> chr2)
>> > myregions_RD <- myregions_RD[which(width(myregions_RD)<=300),]
>>
>> > ### this doesn't work - reduce doesn't like a space without any elements
>> > reduce(myregions_RD)
>> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism
>>
>> > ### workaround - drop the unused space names
>> > myregions_RD <-
>> RangedData(IRanges(start=start(myregions_RD),end=end(myregions_RD)),space=as.character(space(myregions_RD)),strand=myregions_RD$strand
>>   )
>>
>> > ### now it works
>> > reduce(myregions_RD)
>> RangedData with 1 row and 1 value column across 1 space
>>        space     ranges |      strand
>>  <character>  <IRanges> | <character>
>> 1        chr1 [101, 300] |           +
>>
>> > sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] IRanges_1.8.9
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
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