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Feature/mouse #53

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merged 13 commits into from
Apr 4, 2020
Merged

Feature/mouse #53

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4fcfc8a
v1.2.4
marcmaxson Mar 3, 2020
ed823c6
v1.2.4 tweaks
marcmaxson Mar 10, 2020
af7ef70
unit testing
marcmaxson Mar 10, 2020
901d864
unit test fix
marcmaxson Mar 10, 2020
f3f0f9d
Merge branch 'master' into dev
Mar 10, 2020
e323e4a
readthedocs fix
marcmaxson Mar 11, 2020
9d9d3c8
Merge branch 'dev' of https://github.com/LifeEGX/methylprep into dev
marcmaxson Mar 11, 2020
2c47ade
better readthedocs autosummary
marcmaxson Mar 11, 2020
a7f35bd
pval probe detection
marcmaxson Mar 26, 2020
fa7218f
mouse array working (RND1) except for 940 failed probes
marcmaxson Mar 28, 2020
3d39c3c
fixed pval probe detection bug where manifest and idat probe names do…
marcmaxson Apr 3, 2020
ed50225
one test failed; fixed snp + control probe case in probes.py
marcmaxson Apr 3, 2020
fc9b573
Merge branch 'master' into feature/mouse
Apr 3, 2020
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fixed pval probe detection bug where manifest and idat probe names do… 
…n't match
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@marcmaxson
marcmaxson committed Apr 3, 2020
commit 3d39c3c1244ae15f1a0c626221f7aad5c8d53a46
8 changes: 6 additions & 2 deletions methylprep/processing/p_value_probe_detection.py
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Expand Up @@ -125,14 +125,18 @@ def _pval_sesame(data_containers):
return pval


def _pval_sesame_preprocess(data_container, column='mean_value', probe_column='IlmnID'):
def _pval_sesame_preprocess(data_container, column='mean_value'):
"""Performs p-value detection of low signal/noise probes. This ONE SAMPLE version uses meth/unmeth before it is contructed into a _SampleDataContainer__data_frame.
- returns a dataframe of probes and their detected p-value levels.
- this will be saved to the csv output, so it can be used to drop probes at later step.
- output: index are probes (IlmnID); one column [poobah_pval] contains the sample p-values."""
- output: index are probes (IlmnID or illumina_id); one column [poobah_pval] contains the sample p-values."""
meth = data_container.methylated.data_frame
unmeth = data_container.unmethylated.data_frame
manifest = data_container.manifest.data_frame[['Infinium_Design_Type','Color_Channel']]
if manifest.index.name != meth.index.name or manifest.index.name != unmeth.index.name:
raise KeyError(f"manifest probe_column ({manifest.dataframe.index.name}) does not match meth/unmeth probe names from idats ({meth.index.name}).")
probe_column = manifest.index.name

IG = manifest[(manifest['Color_Channel']=='Grn') & (manifest['Infinium_Design_Type']=='I')]
IR = manifest[(manifest['Color_Channel']=='Red') & (manifest['Infinium_Design_Type']=='I')]
II = manifest[manifest['Infinium_Design_Type']=='II']
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4 changes: 1 addition & 3 deletions methylprep/processing/pipeline.py
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Expand Up @@ -436,10 +436,8 @@ def preprocess(self):
uncorrected_unmeth = self.unmethylated.data_frame.copy()

if self.pval == True:
# (self.methylated.data_frame, self.unmethylated.data_frame)
pval_probes_df = _pval_sesame_preprocess(self)
# df with one column named 'poobah_pval'
# missing: how to merge this df into the data_frame and actually drop probes
# output: df with one column named 'poobah_pval'

preprocess_noob(self) # apply corrections: bg subtract, then noob (in preprocess.py)

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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -3,7 +3,7 @@

setup(
name='methylprep',
version='1.2.5',
version='1.2.8',
description='Python-based Illumina methylation array preprocessing software',
long_description=open('README.md').read(),
long_description_content_type='text/markdown',
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