[ENH] Adds parameter for normalizing donor microarray expression values #90
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For normalization gene expression values across regions for each donor prior to donor aggregation.
Codecov Report
@@ Coverage Diff @@
## master #90 +/- ##
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+ Coverage 90.57% 91.05% +0.48%
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Files 32 31 -1
Lines 1730 1812 +82
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+ Hits 1567 1650 +83
+ Misses 163 162 -1
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All functions are moved (including tests) and imports are updated as necessary. Also adds an additional 'batch' option for normalize_expression() function to use linear models to residualize donor differences.
NaN handling is completely performed by normalize_expression()
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I think within-sample normalization should be relegated to a separate PR since this one is already a bit monstrous. It's different, conceptually, from what |
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Closes #45.
Adds new
donor_normparameter toabagen.get_expression_data()(andabagenCLI command) that controls how donor microarray values are normalized prior to aggregation.Current options include 'srs' (scaled robust sigmoid) and 'zscore'.
To do:
batchnormalization (i.e., linear models across donors)