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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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