Currently, IRanges does not play well with dplyr dataframes, e.g.:
library(IRanges)
library(dplyr)
df = tbl_df(data.frame(
id=c(1,2,3),
group=c('a','b','c')
))
> DataFrame(df)
library(dplyr)
> DataFrame(df)
DataFrame with 2 rows and 1 column
Error in `rownames<-`(`*tmp*`, value = c("id", "group")) :
length of 'dimnames' [1] not equal to array extent
Calls: <Anonymous> -> <Anonymous> -> rownames<- -> rownames<-
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] dplyr_0.2 IRanges_1.99.18 S4Vectors_0.1.2
BiocGenerics_0.11.3
[5] vimcom_1.0-0 setwidth_1.0-3 colorout_1.0-3
loaded via a namespace (and not attached):
[1] assertthat_0.1 Rcpp_0.11.2 stats4_3.1.0 tools_3.1.0
Any easy work-around to this is simply to cast the dplyr dataframes to a
regular dataframe before passing them in to IRange constructors, etc.:
> DataFrame(as.data.frame(df))
DataFrame with 3 rows and 2 columns
id group
<numeric> <factor>
1 1 a
2 2 b
3 3 c
However, since tbl_df's are dataframes themselves, it seems like it should
not be too difficult to support them natively, or at the very least, check
for/cast them to data frames in IRanges.
Is there any chance this can be supported in future versions of IRanges?
Regards,
Keith
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