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
________________________________________
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Marcin
Kosiński [m.p.kosin...@gmail.com]
Sent: Sunday, November 22, 2015 11:37 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Is there a way to change the name of R package that
is already published on bioconductor?
Hi Herve,
I think I would like to proceed with such technical possibility.
I'd like to keep consistency with the RTCGA.miRNASeq package that I am
uploading to bioconductor with issue 1335.
Can we schedule such operation?
Best,
Marcin
Hi Dario,
Do you want to tell me that there is a possibility to load RNASeq datasets
for all available 38 cancer types/cohorts from the last release date
(21-08-2015) of datasets from The Cancer Genome Atlas with the use of
AnnotationHub?
Is it as simple as:
library(AnnotationHub)
BRCA.RNASeq -> x
?
Best,
Marcin
2015-11-17 0:00 GMT+01:00 Dario Strbenac <dstr7...@uni.sydney.edu.au>:
Hello,
How does your package differ to importing GSE62944 into R with
AnnotationHub
http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It
seems like unnecessary duplication.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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