Hi Dario,
I am the maintainer of chimera package
thank for the info I am going to check which is the problem in
importFusionData.
There is only one example of data import, because of limits in package size.
An other example can be retrieved from:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download";,
"Chimeric.out.junction.zip", mode="wb")
I check the example:
tmp <- importFusionData("fusionmap",
paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport",
sep=""), org="hg19")
and it seems to import correctly the fusionmap data.
Same happens with:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download";,
"Chimeric.out.junction.zip", mode="wb")
unzip("Chimeric.out.junction.zip")
tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19",
min.support=100)
Could please send me the code you have run and could you please describe
the issue you encountered?
Cheers
Raf
Today's Topics:
1. Re: chimera Attempts to Open Non-existent File (Dario Strbenac)
Message: 1
Date: Sun, 6 Nov 2016 11:00:07 +0000
From: Dario Strbenac <dstr7...@uni.sydney.edu.au>
To: "bioc-devel@r-project.org" <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] chimera Attempts to Open Non-existent File
Message-ID:
<mwhpr01mb27010078d6700175272f5a9ccd...@mwhpr01mb2701.prod.exchangelabs.com>
Content-Type: text/plain; charset="us-ascii"
Good day,
The examples section of importFusionData is almost entirely commented out, so
it's unclear whether it works. Since a lot of the package code is never run by
R CMD check and the test coverage is 0%, it's plausibly a package development
issue.
-------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
--
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
Tel. ++39 0116706454
Fax ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calog...@unito.it
raffaele.calog...@gmail.com
www: http://www.bioinformatica.unito.it
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