[BioC] IRanges glitch: error restoring saved RangedData object
Martin Morgan
mtmorgan at fhcrc.org
Sat Aug 14 00:17:47 CEST 2010
Hi Michael --
I think this is a problem in the methods package; the 'show' method
found is for DataTable, instead of RangedData. I'll pursue this
elsewhere and let you know what comes of it.
Martin
On 08/13/2010 02:44 AM, Michael Dondrup wrote:
> Hi,
> I guess I found a little bug in IRanges. When loading a saved RangedData object before loading library(IRanges)
> before, then IRanges is loaded automatically but the RangeData object is rendered unusable. Only restarting R lets me access
> the object.
> The following code reproduces this:
> $ R --vanilla
> version 2.11.1 (2010-05-31)...
>> library(IRanges)
>> rd = RangedData(IRanges(start=c(1:10), width=2, names=letters[1:10]), space="chr1", score=rnorm(10))
>> rd
> RangedData with 10 rows and 1 value column across 1 space
> space ranges | score
> <character> <IRanges> | <numeric>
> a chr1 [ 1, 2] | -0.79949926
> b chr1 [ 2, 3] | 1.09152227
> c chr1 [ 3, 4] | 0.19032854
> d chr1 [ 4, 5] | 0.37248408
> e chr1 [ 5, 6] | 0.68396618
> f chr1 [ 6, 7] | -1.19804918
> g chr1 [ 7, 8] | 0.01221636
> h chr1 [ 8, 9] | 0.66203090
> i chr1 [ 9, 10] | 0.39848133
> j chr1 [10, 11] | 0.15233945
>> save(rd, file="rd.r")
>> q()
> # restart R
> $ R --vanilla
>> load("rd.r")
>> rd
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
> rbind, rep.int, table
>
> RangedData with 10 rows and 1 column
> Error in dimnames(x) <- dn :
> length of 'dimnames' [1] not equal to array extent
>>
>
> Note that this depends on presence of rownames. If you make an object
> rd = RangedData(IRanges(start=c(1:10), width=2), space="chr1", score=rnorm(10))
> without named IRanges, the result after loading is
>> rd
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
> rbind, rep.int, table
>
> RangedData with 10 rows and 1 column
> chr1
> <RangedData>
> 1 ########
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> 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=en_US.UTF-8
> [7] LC_PAPER=no_NO.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=no_NO.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] IRanges_1.6.11
>>
>
>
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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