On Oct 1, 2017, at 9:29 PM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:
I cannot speak for the core team.
You should separate the data from the software methods and provide a data
package containing the MAFs. This has the additional advantage of
separating versionning of the mutation data from your software. As a data
package this does not sound extensive; the largest dataset is 3.7Mb. There
is a potential privacy problem with sharing mutations, but I don't know at
what level the mutations are described. I assume you have considered this?
Best,
Kasper
On Sun, Oct 1, 2017 at 9:16 PM, Anand MT <anand_mt at hotmail.com> wrote:
Hi all,
I maintain maftools package which offers multitude of functions to perform
various analyses and visualization of MAF (Mutation Annotation Format)
files from cancer cohorts.
In the upcoming bioconductor release, I plan to include all MAFs from 32
TCGA cohorts as a part of the package. These tcga mafs will be stored as
MAF objects containing curated somatic mutations along with clinical
information in the extdata directory and can be loaded via a ?tcga_load?
function.
I think this will help many researchers working with tcga mutation data
and saves the time and hassle of going through various databases to search
and assemble. I believe this also helps in reproducible research.
However, size of these MAF objects vary according to the cohorts size and
mutation burden; with LAML (leukemia) being the smallest (91 kb) and LUAD
(Lung Adeno Carcinoma) being the largest (3.7 mb). Also including these
MAFs increases package size to 46 mb (from 7mb without theses datasets).
My question is,
* is it okay for a package to be of this size ?
* I haven't tried to push these commits to repository yet, but in case
git rejects my push due to size limit, is it possible to make an exception,
given the scenario ?
If this can't be done in any ways or if it breaks any rules of package
guidelines, I don't mind dropping the idea either.
Thanks.
-Anand.
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