Thanks, this is fixed in 1.22.8 (to appear).


On Fri, May 30, 2014 at 5:49 AM, Ludo Pagie <ludo.pagie@gmail.com> wrote:

> Dear all,
>
> I'm using GRanges objects ('df') to store read counts on 7M genomic
> regions. I found that the colnames of mcols(df) do not behave nicely
> when using the names are not 'syntactic valid'. But this behavior
> depends on whether columns are referenced using '[[' or using '['. I
> would think this is not intended to work like this?
>
> ###############
> # initialize a DataFrame with 3 columns and 2 rows. specify colnames
> should not be checked for validity
> df <- DataFrame(matrix(ncol=3, nrow=2), check.names=FALSE)
> # assign names which would be changed if "check.names=TRUE"
> names(df) <- c(1:3)
> # names are as specified:
> df
> #DataFrame with 2 rows and 3 columns
> #          1         2         3
> #  <logical> <logical> <logical>
> #1        NA        NA        NA
> #2        NA        NA        NA
>
> # assign values to 1st column using '['
> df[,1] <- 1:2
> # df still has original names:
> df
> #DataFrame with 2 rows and 3 columns
> #          1         2         3
> #  <integer> <logical> <logical>
> #1         1        NA        NA
> #2         2        NA        NA
>
> # assign using '[['
> df[[2]] <- 3:4
> # colnames are now changed:
> df
> #DataFrame with 2 rows and 3 columns
> #         X1        X2        X3
> #  <integer> <integer> <logical>
> #1         1         3        NA
> #2         2         4        NA
>
> # sessionInfo:
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] IRanges_1.20.6     BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.2
>
> ########################################################
>
> Thanks, Ludo
>
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