[Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

Hi Marcin,

BTW I noticed that RTCGA has no biocViews (only Software). Populating
the biocViews field with appropriate and specific terms will make
your packages show up in the corresponding views here

  http://bioconductor.org/packages/release/BiocViews.html#___Software

and thus will greatly improve the chances that the user in the need
of functionalities like the ones you provide will discover your package.

Cheers,
H.


On 11/22/2015 10:39 AM, Morgan, Martin wrote:

Marcin -- I join with Herve in strongly discouraging you from this
approach. Because you wish only to change upper versus lower case of your
package name, and because some operating systems ignore case, your package
will go through a release where it is not available under either upper- or
lower-case variant. This will confuse and alienate your users, even more
than changing the package name to something completely different. There are
a number of packages, including some of our own, where the name could have
been chosen more carefully, but we have learned to live with our changes of
mind. After all, you can still claim to be consistent with the naming
convention of the RTCGA.clinical and RTCGA.mutations package ;)

I guess Dario was referring to

   library(AnnotationHub)
   hub = AnnotationHub()
   eset = query(hub, "GSE62944")[[1]]

with

eset

ExpressionSet (storageMode: lockedEnvironment)
assayData: 23368 features, 7706 samples
   element names: exprs
protocolData: none
phenoData
   sampleNames: TCGA-02-0047-01A-01R-1849-01
     TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706
     total)
   varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421
     total)
   varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:

table(eset$CancerType)

BLCA BRCA COAD  GBM HNSC KICH KIRC KIRP LAML  LGG LIHC LUAD LUSC   OV
PRAD READ
  273 1082  468  170  481   66  540  226  164  528  212  514  490  344
423  164
SKCM STAD THCA UCEC
  373  146  506  536

print(object.size(eset), units="auto")

264.5 Mb

ov = eset[, eset$CancerType == "OV"]   ## ovarian samples

The data are Rsubread summarized counts from before the May update. In
the near term, we are actively expanding offerings derived from that GSE to
include the May update; this is in conjunction with efforts to develop an
'ExperimentHub' analog of AnnotationHub, for more experiment-centric,
heavily curated resources.

It is a little unclear whether the AnnotationHub and your data are
redundant or complementary, and whether they can be combined into a single
offering. One philosophical difference is the use of semantically rich and
integrated ExpressionSet versus basic data structures (data.frame, in your
case). We also differ in when we separate data into cancer types; we opted
for the entire data set because it is not impossibly large. And our data
are AnnotationHub-based rather than package-based. Obviously, avoiding
redundant access to the same data is beneficial. One possibility is to
collaboratively curate the data into AnnotationHub / ExperimentHub
resources, and to tailor access via packages that reference the resource
(e.g., one can retrieve the GRASP2 data base through AnnotationHub as
resource AH21414, or via grasp2db::GRASP2(); the latter comes with
documentation for manipulating the resource).

It seems like there are similar opportunities for collaboration and
reduced redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks
packages.

Martin Morgan
Bioconductor

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

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