Revision history for GO-TermFinder group of modules.
0.64 Sun Aug 15 23:30:32 2004
- GO::View
Added the ability to create postscript output from
GO::View - simply change the makePs attribute in the
GoView.conf file to a '1', and if you run batchGoView.pl, you
should get a postcript file as well as png or gif images. The
Postscript is not perfect, because the GraphViz interface
doesn't seem to allow me to modify the page size (even though
it says I should be able to), so I have restricted the size of the
image to try and get it to fit on one page. Suggestions as to how to
make the postscript feature more robust would be appreciated.
Added in copious comments to GO::View, so that most of it can
actually be understood my regular programmers - performed some
cleanups or unnecessary or obfuscated code in the process.
Significant refactoring of this module is next on the agenda.
0.63 Wed Aug 11 11:16:23 2004
- GO::View
Fix to bug that was causing some significant nodes to not
have the correct color, and thus making the image somewhat
misleading - thanks to the folks at Princeton for spotting it,
and to Shuai Weng at SGD for providing a fix in record time.
fixed bug in reading of configuration file, that resulted from
minMapWidth being a substring of minMapWidth4OneLineKey. This
now stops a warning being printed.
Added some comments to GO::View, as a start to begin to fully
comment all the code - there's a long way to go until I
understand fully how GO::View works. Then I can add
postscript output for publication qaulity figures...
0.62 Wed Jul 28 11:46:08 2004
No major new functionality - small bug fix release
- AnnotationParser.pm
fixed capitalization bugs when calling goidsByDatabaseId() in
nameIsAnnotated() instead of goIdsByDatabaseId() on lines 1592
and 1617 - thanks to lfriedl@cs.umass.edu for spotting this.
- GoView.conf
Fixed typo in GoView.conf : totalNumGene should be
totalNumGenes - thanks to John Matese for spotting this one.
- GO::TermFinder
Made __databaseIds() method of GO::TermFinder public, and
named it genesDatabaseIds, as I realized it is the only way
that a client can determine how many genes were actually used
when calculating p-values. Before, I was using the number of
genes that were passed in, but they will get collapsed if more
than one maps to the same databaseId.
- batchGOView.pl
Modified batchGOView.pl to use the genesDatabaseIds method.
Removed its use of the CategorizeGenes function in
GO::Utils::General, as I don't think was was any reasonable
logic for using it (that I can remember).
- GO::TermFinder
Fixed lots of spurious warnings that were due to checking the
state of a variable before it had been set, when using a user
defined background population - thanks to Jeremy Gollub for
spotting this one.
- GO::TermFinder
If a gene is padded in multiple times in either the list of
genes of interest, or the background population, you should
only be warned about that gene once for each list, rather than
every time the gene is encountered.
0.61 Fri May 7 11:23:36 2004
- GO::TermFinder
Made one line optimization to calculation of p-value using the
hypergeometric distribution, such that it is on average about
twice as fast.
0.60 Wed May 5 15:04:06 2004
- GO::TermFinder
The multiple hypothesis correction is no longer done using the
custom method, but instead uses a Bonferroni correction.
Correcting p-values by running simulations is now available,
to allow you to control the Family Wise Error rate.
Added the ability to calculate the False Discovery Rate, as a
potential means of avoiding the whole p-value problem.
see the pod for GO::TermFinder, as well as docs/GO-TermFinder.doc
for more information on these.
- tools
updated the batchGOView.pl tool, and the analyze.pl tool, in
the examples directory, to support printing out of the False
Discovery Rate if calculated. They also both use the newly
created GO::TermFinderReport::Text object, to consolidate code, and
to keep their reports consistent with one another.
- README
Tried to make it a little clearer as to how to install the libraries.
0.50 Tue Dec 16 17:34:50 2003
Big news is that a version of Shuai Weng's (from SGD) GO::View
module has been added in, which can create a graphic
representation of the results of GO::TermFinder. This gives a
much better way to intuitively look at the results. A bunch
of other stuff was added in to support this, including a batch
processor that will generate an html pages with a graphic for
any number of input lists of genes. See batchGOView.pl and
examples.html in the examples directory.
- GO::TermFinder
Fixed a nasty bug that was actually due to a bug in Perl (I
swear!) that meant that clients of the GO::TermFinder would
have a runtime error if they did not recognize one or more of
the genes that it was provided with. This should no longer
happen, and I have written additional tests to make sure it
never happens again!
0.40 Tue Dec 2 18:41:10 2003
- GO::TermFinder
Added in the ability to define a subpopulation of genes as the
background from which the interesting genes were drawn. See
pod for constuctor of GO::TermFinder for more details.
0.30 Wed Nov 26 11:48:57 2003
- GO::AnnotationProvider::AnnotationParser
Extensive reworking of the code, such that it is now case
insensitive, with certain caveats. See the pod for that
module for more details.
- GO::TermFinder
No longer considers the root node, or its child (the aspect)
as hypotheses, as they are known a priori to have a p-value of
1.
- GO::Node
Added lengthOfShortestPathToRoot and meanLengthOfPathsToRoot
methods.
- added in new tests for the AnnotationParser that make sure
that the behaviour with respect to case insensitivity is
correct.
0.23 Sat Nov 1 11:56:43 2003
- GO::OntologyProvider::OntologyParser;
Added in check that a given non-comment line can actually have
a GOID extracted, which makes the error a more informative
when such a line is encountered, due to an error in an
ontology file.
0.22 Sun Oct 19 16:54:38 2003
- GO::TermFinder
Fix for test that could occasionally fail that relied on
the sort order of the pValue array when two items had the
same pvalue. It now sorts such cases explicitly by goid,
so the result should always be the same.
0.21 Thu Oct 16 19:00:14 2003
- GO::TermFinder
Fix for situation when a gene identifier wasn't recognized,
but wasn't handled properly - thanks to Shuai Weng for bring
it to my attention.
Cleaned up the code that calculates the p-values to make it
easier to write a test-suite, which will allow me to make
other desired changes with more confidence.
- tests
Created tests for the GO::TermFinder module itself, that pass
under both OSX and Solaris in my testing - this should make it
much easier to modify in future with less concern for failing
to notice new bugs.
- examples
Added a new example, that makes it easier to analyze multiple
files of gene names.
- suppressed some warnings that occured due to some undefs
being used.
- fixed some documentation typos
0.2 Mon Apr 14 17:55:28 2003
- added in code such that the findTerms() method will return
enough data for you to be able to work out which genes in
the list you provided were annotated to which GO nodes.
- started some work on Annotation, AnnotatedGene, and
Reference objects. Nothing is using them yet though.
- added in over 100 tests(!). Still lots more to do, but this
should help keep the code honest...
0.1 Fri Mar 7 13:51:32 2003
- original version; created by h2xs 1.21 with options
-n GO-TermFinder -X