[BioC] GRangesList replacement method bug

[Richard Bourgon]

BioC team:

I encountered a bug with replacement methods for GRangesList objects (see below for code). 

Basically, you can set to non-existant elementMetaData columns for a GRanges object, but not if it is a part of a GRangesList. Setting to already existing columns is fine, however.

Richard Bourgon, Ph.D.
Genentech, Inc.
Bioinformatics & Computational Biology
1 DNA Way, MS 93
South San Francisco, CA 94080-4990
(650) 467-2064

***

gr <- GRanges( "a", IRanges(1,10), x = TRUE )
grl <- GRangesList( y = gr, z = gr )
values( grl[["y"]] )$x <- FALSE # Fine for existing column
values( grl[["y"]] )$w <- FALSE # Fails for new column

Error in .Method(..., deparse.level = deparse.level) :
number of columns for arg 2 do not match those of first arg

values( gr )$w <- FALSE # No problem with new column here
sessionInfo()

R version 2.14.0 (2011-10-31)
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=C                 LC_NAME=C                  LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] datasets  utils     grDevices graphics  stats     methods   base

other attached packages:
[1] rtracklayer_1.14.4    RCurl_1.8-0           bitops_1.0-4.1        GenomicRanges_1.6.4
[5] IRanges_1.12.5        gdata_2.8.2           BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] Biobase_2.14.0    Biostrings_2.22.0 BSgenome_1.22.0   gtools_2.6.2      tools_2.14.0
[6] XML_3.6-2         zlibbioc_1.0.0