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Use at least 20 samples for all splicing calculations #311

Merged
merged 44 commits into from
Jun 12, 2015
Merged

Use at least 20 samples for all splicing calculations #311

merged 44 commits into from
Jun 12, 2015

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olgabot
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@olgabot olgabot commented Jun 9, 2015

e.g. NMF space and modalities

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olgabot commented Jun 9, 2015

  • Is it mergable?
  • Did it pass the tests?
  • If it introduces new functionality in is it tested?
    Check for code coverage. To run code coverage on only the file you changed,
    for example flotilla/compute/splicing.py, use this command:
    py.test --cov flotilla/compute/splicing.py --cov-report term-missing flotilla/test/compute/test_splicing.py
    which will show you which lines aren't covered by the tests.
  • Do the new functions have descriptive
    numpydoc
    style docstrings?
  • If it adds a new feature, is it documented as an IPython Notebook in
    examples/, and is that notebook added to doc/tutorial.rst?
  • If it adds a new plot, is it documented in the gallery, as a .py file
    in examples/?
  • Is it well formatted? Look at the output of make lint.
  • Is it documented in the doc/releases/?
  • Was a spellchecker run on the source code and documentation after
    changes were made?

olgabot added 27 commits June 9, 2015 11:26
@olgabot
change number of samples to 50 for splicing testing
304959a
@olgabot
use n=20 as default instead of n=0.5
75f749e
@olgabot
fix tests for splicing modalities and NMF space
5c7cea3
@olgabot
update all NMF and modality calculations to require 20 samples, fix b…
7761406 
…ug for NMF space labeling
@olgabot
change number of samples to 50 for splicing testing
0a0e9ac
@olgabot
use n=20 as default instead of n=0.5
6946175
@olgabot
fix tests for splicing modalities and NMF space
65703c4
@olgabot
if there are zero non-NA values in a dataset, make sure all its log b…
5bed758 
…fs are NA
@olgabot
Merge remote-tracking branch 'origin/splicing_min20' into splicing_min20
0f57cf9 
* origin/splicing_min20:
  fix tests for splicing modalities and NMF space
  use n=20 as default instead of n=0.5
  change number of samples to 50 for splicing testing
  update all NMF and modality calculations to require 20 samples, fix bug for NMF space labeling
@olgabot
don't estimate modalities on data iwth no counts
e742b7c
@olgabot
actually get column names instead of boolean series
54b6b78
@olgabot
get proper columns for ambiguous_columns and use reindex for just col…
da210e4 
…umns instead of reindex_like for everything
@olgabot
intersect non_na_columns and ambiguous_columns to get only the column…
732aa6d 
…s that are valid in data2
@olgabot
modality_assignements is a series
a6e1f52
@olgabot
return bayesfactors not estimated modalities
548184e
@olgabot
Return dataframe with the same columns, but everything without enough…
30b324c 
… data gets a NA
@olgabot
concatenate 1 and 2 not just 1...
9777613
@olgabot
separate the fit transform code to have a subroutine for each individ…
b4908c6 
…ual step
@olgabot
Fix concatenating of two and one-paramter models
0917709
@olgabot
Remove old code that was commented out
2b4ab88
@olgabot
Add assign_modalities function to operate on bayes factor dataframes
b009f3f
@olgabot
bayes_factors --> log2_bayes_factors (since that's the truth)
8d7309d
@olgabot
make separate modality_scores function that modality_assignments calls
1e1c20b
@olgabot
modality_scores --> modality_log2bf
e068e07
@olgabot
change naming of modalities in test to the new names
4ed8906
@olgabot
Change test of fit_Transform to only test getting the scores
98193d2
@olgabot
Actually test modality_log2bf and modality_assignments
9f76d4f
olgabot added 16 commits June 10, 2015 19:33
@olgabot
actually test assign_modalities in compute.splicing
512fb85
@olgabot
use estimator instead of self testing object
7e97269
@olgabot
self --> splicing so don't use test object
9ce0a6b
@olgabot
change model variable names to reflect psi~1, psi~0 renaming
bc40383
@olgabot
only check modality correctness on the events which had enough sample…
5891423 
…s to check modalities on
@olgabot
The "true modalities" are only what kind of beta distribution was giv…
24d70c7 
…en, the exact numbers are by chance. so check estimation of modalities using the algorithm itself
@olgabot
Add a "positive control" test for modalities. If this one doesn't pas…
4a6f64c 
…s, then ..... that's bad
@olgabot
Add -v flag for verbose pytest output so we know what's failing even …
9c0e72e 
…while tests are running
@olgabot
simplify names to test and true
3743853
@olgabot
correct docstring
7c84e4d
@olgabot
don't do NMF transitions if the dataframe is entirely NA
90e584a
@olgabot
remove big nmf space transitions because the choice of "big" is stil …
9fece26 
…arbitrary... should be more robust
@olgabot
remove big nmf space transitions because the choice of "big" is stil …
a251090 
…arbitrary... should be more robust
@olgabot
pep8 fixes
52aaafc
@olgabot
Remove big_nmf_space transitions because the cutoff is too arbitrary
6558f8b
@olgabot
Add release notes about modalities, minimum20 samples for splicnig an…
769d7a3 
…d nmf
olgabot added a commit that referenced this pull request Jun 12, 2015
@olgabot
Merge pull request #311 from YeoLab/splicing_min20
77e19d0 
Use at least 20 samples for all splicing calculations
@olgabot olgabot merged commit 77e19d0 into master Jun 12, 2015
@olgabot olgabot deleted the splicing_min20 branch June 12, 2015 04:22
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