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

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

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
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