[BioC] DataFrame(..., check.names=F); colnames change when assign data using '[[', not when using '[,]'

[Ludo Pagie]

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