Question: Old jmosaics working package
0
20 months ago by
james.dalgleish30 wrote:

I've had a hard time finding it, but is there a jmosaics package that is version 1.1.0? I've been trying to find it and had old code that required it's use for chipseq.

http://www.bioconductor.org/packages//2.13/bioc/html/jmosaics.html The package binary (zip) listed here doesn't actually contain all the needed functions to run tutorial code, for example:

> bin1 <- readBins(type = c("chip","input"),
+                  fileName = c(system.file(file.path("extdata","h3k27me3_chip_chr10.txt"),
+                                           package="jmosaics"),
+                               system.file(file.path("extdata","h3k27me3_input_chr10.txt"),
+                                           package="jmosaics")))
Info: reading and preprocessing bin-level data...
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
line 1 did not have 3 elements

Upon inspecting the package, the namespace has the following contents:

import(mosaics)
export(jmosaicsPattern,
)

The R directory doesn't have the functions I'm looking for, as far as I can tell and I can't pull up documentation for the readBins function.

So the key question is... where is the old version (1.1.0) that actually had all the functions needed to run the tutorial code?  I can't get the old versions because the bioconductor github mirror doesn't have the file any longer.

jmosaics • 358 views
modified 20 months ago • written 20 months ago by james.dalgleish30

Is there a replacement that does something similar? I've never seen anything quite like it previously.

0
20 months ago by
United States
James W. MacDonald51k wrote:

The jmosaics package was deprecated in 3.3 and removed for the 3.4 release. So technically it's no longer a Bioconductor package, and no longer tracked in the Bioc git server.  Nor is it supported in any way on this support site. In addition, the git mirror is defunct as well. We now use git for version control and if I am not mistaken, the only way for non-developers to access a git repository is if the developer also maintains a github version as well.

You can install any of the versions of R that correspond to any of the Bioc versions that did include jmosaics and install via biocLite, but otherwise you are unlikely to get any between-release versions of that package.

1

Actually, it's still alive, for the moment, in svn

svn checkout https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/jmosaics


jmosaics\$ svn diff -c75270 DESCRIPTION
Index: DESCRIPTION
===================================================================
--- DESCRIPTION    (revision 75269)
+++ DESCRIPTION    (revision 75270)
@@ -1,7 +1,7 @@
Package: jmosaics
Type: Package
Title: Joint analysis of multiple ChIP-Seq data sets
-Version: 1.0.0
+Version: 1.1.0
Date: 2013-01-29
Author: Xin Zeng
Maintainer: Xin Zeng <xinzeng@stat.wisc.edu>


So it looks like the source code is available as

svn checkout -r75270 https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/jmosaics


(There were no commits on master between this version bump and the 1.2.0 release, so except for the version bump 1.1.0 and 1.2.0 are the same).