gatk-3.8

Commit Graph

Author	SHA1	Message	Date
chartl	a79967d9af	After extensive testing of MannWhitneyU: - Verified that exact calculations do agree with R's dwilcox() - Verified that exact calculations do not agree with R's wilcox.test + This is because R does a correction, and calculates CDFs rather than PDFs (e.g. sums over dwilcox() values) - Can now specify MWU to calculate cumulative exact tests, rather than point probabilities - Z-scores are now calculated properly for exact tests + Previously, z-values calculated by inverting normal CDF from U-statistic PDF + Now both inversions are done, with a smart heuristic (biased variance) to make the point-calculated Z-value more accurate + Additional tests git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5911 348d0f76-0448-11de-a6fe-93d51630548a	2011-06-01 15:51:27 +00:00
chartl	7ff5375493	Removing build-killing dependency on a private package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5851 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-23 18:13:15 +00:00
chartl	0b07373909	Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods. Also allows for the slightly more awesome name "MWUnitTest" git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5850 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-23 18:06:05 +00:00

Author

SHA1

Message

Date

chartl

a79967d9af

After extensive testing of MannWhitneyU:

- Verified that exact calculations do agree with R's dwilcox()
 - Verified that exact calculations do not agree with R's wilcox.test
   + This is because R does a correction, and calculates CDFs rather than PDFs (e.g. sums over dwilcox() values)
 - Can now specify MWU to calculate cumulative exact tests, rather than point probabilities
 - Z-scores are now calculated properly for exact tests
   + Previously, z-values calculated by inverting normal CDF from U-statistic PDF
   + Now both inversions are done, with a smart heuristic (biased variance) to make the point-calculated Z-value more accurate
   + Additional tests



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5911 348d0f76-0448-11de-a6fe-93d51630548a

2011-06-01 15:51:27 +00:00

chartl

7ff5375493

Removing build-killing dependency on a private package.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5851 348d0f76-0448-11de-a6fe-93d51630548a

2011-05-23 18:13:15 +00:00

chartl

0b07373909

Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.

Also allows for the slightly more awesome name "MWUnitTest"



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5850 348d0f76-0448-11de-a6fe-93d51630548a

2011-05-23 18:06:05 +00:00

3 Commits (dcd13060e11278d40a4121122dccc961e7bb0c42)