[Bioc-devel] DataFrame's do not like ordered factors

[Steve Lianoglou]

Thanks for the quick check, Hervé.

R-3.0 is shaping up to be a good one ... I mean, I was excited for the
64-bit integer support, but now ... this is already fixed? yes!

:-)

Cheers,
-steve

On Wed, Mar 6, 2013 at 12:42 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> Hi Steve,
>
>
> On 03/06/2013 09:10 AM, Steve Lianoglou wrote:
>>
>> I don't think I've seen this one discussed before .. consider:
>>
>> ========= Reproduce me ===========
>> library(IRanges)
>> df1 <- data.frame(a=rnorm(10), b=head(letters, 10))
>> df2 <- transform(df1, b=factor(b))
>> df3 <- transform(df1, b=factor(b, sample(b), ordered=TRUE))
>>
>> DF1 <- DataFrame(df1)
>> DF2 <- DataFrame(df2)
>> DF3 <- DataFrame(df3)
>>
>> ## Now let's take a look at them
>> DF1 ## looks purty
>>
>> DF2 ## looks nice
>>
>> DF3 ## woops!
>>
>> DataFrame with 10 rows and 2 columns
>> Error in matrix(unlist(lapply(object, function(x) paste("<", class(x),  :
>>    length of 'dimnames' [2] not equal to array extent
>> ===================================
>
>
> This problem seems to be gone in BioC devel:
>
>   > DF3
>
>   DataFrame with 10 rows and 2 columns
>                a         b
>        <numeric> <ordered>
>   1  -0.98455768         a
>   2 0.35134835         b
>   3   0.04657733         c
>   4 1.86833121         d
>   5 0.54396927         e
>   6 -0.64201201         f
>   7 0.45709514         g
>   8 0.47964197         h
>   9 -1.37778026         i
>   10  0.07408252         j
>
>   > sessionInfo()
>   R Under development (unstable) (2013-02-19 r62008)
>   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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    [7] LC_PAPER=C                 LC_NAME=C
>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
>   [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>   attached base packages:
>   [1] parallel  stats     graphics  grDevices utils     datasets  methods
>   [8] base
>
>   other attached packages:
>   [1] IRanges_1.17.35    BiocGenerics_0.5.6
>
>   loaded via a namespace (and not attached):
>   [1] stats4_3.0.0 tools_3.0.0
>
> H.
>
>
>>
>> Here it only looks like it's messing w/ the `show` method, but it will
>> bite you in other places where you expect DataFrame's to function "as
>> normal."
>>
>> I'll take a deeper look at this after I get through a deadline for
>> next week, but if someone has some time between now and then ...
>>
>> Relevant info:
>>
>> R version 2.15.2 Patched (2012-11-12 r61105)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> ....
>> other attached packages:
>> [1] IRanges_1.16.6     BiocGenerics_0.4.0 devtools_1.1
>>
>>
>> -steve
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact