[BioC] AnnotatedDataFrame metadata bug?

[Adrienne Stilp]

Hi Bioconductors,

I recently noticed some unexpected behavior for AnnotatedDataFrame metadata. If you have an annotated data frame with metadata and add a new variable whose name is a shortened version of an existing variable, the metadata for the newly-added variable is set to the metadata of the existing variable. Here's an example:

library(Biobase)

annot <- AnnotatedDataFrame(data.frame(myvariable=runif(10)))
varMetadata(annot)["myvariable", "labelDescription"] <- "random samples from a uniform distribution"

annot$myvar <- rnorm(10)
annot$newvar <- rnorm(10)
annot[["myvari"]] <- rnorm(10)

varMetadata(annot)


For me, this last step prints out:

                                     labelDescription
myvariable random samples from a uniform distribution
myvar      random samples from a uniform distribution
newvar                                           <NA>
myvari     random samples from a uniform distribution


even though I've only set the metadata for myvariable.  I would expect that any new variables have NA for metadata, which is true for "newvar" above, but is not the case for the variables whose names are a shortened version of "myvariable" ("myvar" and "myvari"). I end up with misleading or incorrect metadata for the new variables "myvar" and "myvari". The can always be changed later, but I often see what metadata I need to update at the end by checking which have NA labelDescriptions, so these new variables wouldn't show up.


I'm using bioc-devel. Here's the sessionInfo() output:

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Biobase_2.22.0     BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] tools_3.0.2


Thanks,
Adrienne