[BioC] IRanges::rbind with names stopped working
Patrick Aboyoun
paboyoun at fhcrc.org
Wed Feb 3 18:59:56 CET 2010
Robert,
Thanks for the bug report. I noticed the same problem yesterday and
checked in a patch earlier this morning to IRanges in BioC 2.6/R-devel
that corrects this issue. The updated package should be available
tomorrow at bioconductor.org or now via the Bioconductor svn.
library(IRanges, warn.conflicts=FALSE)
rd1 <- RangedData(IRanges(start=1:3,
end=4:6))
rd2 <- RangedData(IRanges(start=1:3,
end=4:6))
rbind(rd1, rd2)
RangedData with 6 rows and 0 value columns across 1 space
space ranges |
<character> <IRanges> |
1 1 [1, 4] |
2 1 [2, 5] |
3 1 [3, 6] |
4 1 [1, 4] |
5 1 [2, 5] |
6 1 [3, 6] |
rd1 <- RangedData(IRanges(start=1:3,
end=4:6,
name=letters[1:3]))
rd2 <- RangedData(IRanges(start=1:3,
end=4:6,
name=letters[4:6]))
rbind(rd1, rd2)
RangedData with 6 rows and 0 value columns across 1 space
space ranges |
<character> <IRanges> |
a 1 [1, 4] |
b 1 [2, 5] |
c 1 [3, 6] |
d 1 [1, 4] |
e 1 [2, 5] |
f 1 [3, 6] |
sessionInfo()
R version 2.11.0 Under development (unstable) (2010-02-01 r51089)
i386-apple-darwin9.8.0
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_1.5.39
Robert Castelo wrote:
> hi Michael, thanks for addressing this quick. it works now in devel for
> the case of RangedData with names but it seems to have broken for the
> case without names, although i'm not sure if maybe this is an intended
> behavior, please let me know.
>
> library(IRanges, warn.conflicts=FALSE)
>
> rd1 <- RangedData(IRanges(start=1:3,
> end=4:6))
> rd2 <- RangedData(IRanges(start=1:3,
> end=4:6))
> rbind(rd1, rd2)
> Error in `rownames<-`(`*tmp*`, value = character(0)) :
> invalid rownames length
>
> rd1 <- RangedData(IRanges(start=1:3,
> end=4:6,
> name=letters[1:3]))
> rd2 <- RangedData(IRanges(start=1:3,
> end=4:6,
> name=letters[4:6]))
> rbind(rd1, rd2)
> RangedData with 6 rows and 0 value columns across 1 space
> space ranges |
> <character> <IRanges> |
> a 1 [1, 4] |
> b 1 [2, 5] |
> c 1 [3, 6] |
> d 1 [1, 4] |
> e 1 [2, 5] |
> f 1 [3, 6] |
>
> sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-10-06 r49948)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] IRanges_1.5.38
>
>
> cheers,
> robert.
>
>
>
> On Tue, 2010-02-02 at 05:11 -0800, Michael Lawrence wrote:
>
>> Sorry, this is fixed now in 2.6.
>>
>> Michael
>>
>> On Tue, Feb 2, 2010 at 3:04 AM, Robert Castelo
>> <robert.castelo at upf.edu> wrote:
>> dear list, and particularly the IRanges developers,
>>
>> i'm porting from BioC 2.4 to BioC 2.6 a script which is doing
>> rbind on
>> two RangedData objects and have noticed that this operation
>> (rbind) now
>> doesn't work when the ranges have names.
>>
>> i'm reproducing below the situation with BioC 2.4, 2.5 and 2.6
>> where for
>> the latter two versions of BioC this functionality fails.
>>
>> *** BioC 2.4
>>
>> library(IRanges, warn.conflicts=FALSE)
>>
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rbind(rd1, rd2)
>> RangedData: 6 ranges by 0 columns
>> columns(0):
>> sequences(0):
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[1:3]))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[4:6]))
>> rbind(rd1, rd2)
>> RangedData: 6 ranges by 0 columns
>> columns(0):
>> sequences(0):
>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
>> base
>>
>> other attached packages:
>> [1] IRanges_1.2.3
>>
>>
>> ** BioC 2.5
>>
>> library(IRanges, warn.conflicts=FALSE)
>>
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rbind(rd1, rd2)
>> RangedData with 6 rows and 0 value columns across 1 space
>> space ranges |
>> <character> <IRanges> |
>> 1 1 [1, 4] |
>> 2 1 [2, 5] |
>> 3 1 [3, 6] |
>> 4 1 [1, 4] |
>> 5 1 [2, 5] |
>> 6 1 [3, 6] |
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[1:3]))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[4:6]))
>> rbind(rd1, rd2)
>> Error in validObject(.Object) :
>> invalid class "RangedData" object: the names of the ranges
>> must equal
>> the rownames
>> sessionInfo()
>> R version 2.10.0 (2009-10-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
>> base
>>
>> other attached packages:
>> [1] IRanges_1.4.10
>>
>> ** BioC 2.6
>>
>> library(IRanges, warn.conflicts=FALSE)
>>
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6))
>> rbind(rd1, rd2)
>> RangedData with 6 rows and 0 value columns across 1 space
>> space ranges |
>> <character> <IRanges> |
>> 1 1 [1, 4] |
>> 2 1 [2, 5] |
>> 3 1 [3, 6] |
>> 4 1 [1, 4] |
>> 5 1 [2, 5] |
>> 6 1 [3, 6] |
>> rd1 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[1:3]))
>> rd2 <- RangedData(IRanges(start=1:3,
>> end=4:6,
>> name=letters[4:6]))
>> rbind(rd1, rd2)
>> Error in validObject(.Object) :
>> invalid class "RangedData" object: the names of the ranges
>> must equal
>> the rownames
>> sessionInfo()
>> R version 2.11.0 Under development (unstable) (2009-10-06
>> r49948)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
>> base
>>
>> other attached packages:
>> [1] IRanges_1.5.37
>>
>>
>> thanks!
>> robert.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>
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