Source

orange-bioinformatics / _bioinformatics / obiGeneSetSig.py

Author Commit Message Labels Comments Date
Marko Toplak
obiGeneSetSig: LLR uses combined standard deviation if a standard deviation for a class was zero (this can happen as an artifict of bootstrap sampling).
Marko Toplak
obiGeneSetSig: added another method based on likelihood ratios by Su et al (2009).
Marko Toplak
obiGeneSetSig: CORG were build a gene too large (fixed). SetSig has the option to check if the examples are exactly alike and discard the distance between them.
Marko Toplak
Added an option in Assess to not ignore umatchable context.
Marko Toplak
obiGeneSetSig: assess now works even if gene matcher did not perfectly match the whole file.
Marko Toplak
SetSig uses statc for pearsonr. Around 10x speedup compared to numpy.
Marko Toplak
obiGeneSetSig: speedup of ASSESS.
Marko Toplak
Speed up PCA and PLS (obiGeneSetSig).
Marko Toplak
Another speedup of SetSig. Now it is 30% faster on DLBCL.tab with no_unknowns=True.
Marko Toplak
Speed up of setsig (obiGeneSetSig).
Marko Toplak
obiGsea.takeClasses: now builds a class value with get_value_from.
Marko Toplak
CV feature build for obiGeneSetSig.
Marko Toplak
obiGeneSetSig: small changes in the interface.
mitar
Restructuring because we will not be using namespaces.