hi Hervé,
thanks for your answer, i also think it isn't clear how one would
automatically combine the object-wise metadata, specially if there were
metadata entries with the same name. just wanted to make sure that this
is a design decision and will remain this way in the future.
best regards,
robert.
On 10/25/2017 05:35 PM, Hervé Pagès wrote:
Hi Robert,
The object-wise metadata doesn't follow any convention and is typically
used to keep track of things like the file the object is coming from
(if any), the date/time it was created, by who, the call that was used
to create it, plus any other relevant information about the object.
It's not clear to me how n-ary operations should combine the object-wise
metadata in general, or that it would make sense to try to propagate
this information from all the input objects to the output object.
Note that AFAIK most unary operations on Annotated derivatives (e.g.
shift()) propagate the object-wise metadata, even though it's not
clear that this information will still be relevant for the transformed
object.
Cheers,
H.
On 10/25/2017 07:39 AM, Robert Castelo wrote:
hi,
i've the following question on how 'S4Vectors::cbind()' works on
'DataFrame' objects.
let's say i have the following two toy 'DataFrame' objects, each of them
including some elementwise and non-elementwise metadata (i hope i'm
using the right terminology!):
library(S4Vectors)
dtf1 <- DataFrame(col1=1:10)
mcols(dtf1) <- DataFrame(ElementwiseMeta="This is column1")
metadata(dtf1) <- list(Meta1="Object storing column1")
dtf2 <- DataFrame(col2=1:10)
mcols(dtf2) <- DataFrame(ElementwiseMeta="This is column2")
metadata(dtf2) <- list(Meta2="Object storing column2")
now use 'cbind()' to combine the two 'DataFrame' objects:
dtf <- cbind(dtf1, dtf2)
the elementwise metadata is also combined:
mcols(dtf)
DataFrame with 2 rows and 1 column
ElementwiseMeta
<character>
1 This is column1
2 This is column2
but the non-elementwise metadata is not:
metadata(dtf)
list()
is there a particular reason why the non-elementwise metadata is not
also combined?
please find my session information below.
thanks!!!
robert.
ps: sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] S4Vectors_0.15.14 BiocGenerics_0.23.4 colorout_1.1-2
loaded via a namespace (and not attached):
[1] compiler_3.4.0
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--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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