Dear list,

I noticed that GRangesList objects are not allowed to have outer
elementMetadata columns with names identical to names of inner
elementMetadata columns (see below)

Is this restriction necessary? And if yes, should identical names raise an
exception at the time of construction rather than further down the line?

Best wishes,

Leonard


> gr <- GRanges("1", IRanges(1, 100), "x" = 1)
> grl <- split(gr, 1)
> mcols(grl)$x <- 1
> grl[1, ]
Error in validObject(.Object) :
  invalid class “GRangesList” object: 'mcols(x)' cannot have columns named
as metadata  columns of unlisted GRanges
>
> sessionInfo()
R version 3.0.0 (2013-04-03)
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] GenomicRanges_1.13.50 XVector_0.1.4         IRanges_1.19.38
[4] BiocGenerics_0.7.5

loaded via a namespace (and not attached):
[1] stats4_3.0.0
>

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