Experimental: imputation of missing genotypes by randomly sampling from
{0,1,2} based on their proportions in the non-missing data
Profile data now saves the score
Cleanup of cache max-memory code
Implemented FMPR fusion in SparSNP, needs testing
Added gamma option to crossval.sh
Made scaling of phenotypes the default for linear regression
Control verbosity and scaling of phenotypes from crossval.sh
Typo fix, thanks to Raj Manrai.
Typo fix in the PDF, thanks to Raj Manrai.
Changed active set method to match that of FMPR, now linear regression results match FMPR and glmnet but at the cost of far more iterations
Fixed stupid but important bug where fusion loss gradient was zero due to
implicit rounding
Made ZERO_THRESH larger
Store more info in params file
Check for convergence in beta
Cleaned up dead code
SparSNP now matches very closely the results of FMPR with fusion penalty in
crossval
Incorporated new convergence test from FMPR-MaxLossDeltaConvergence, matches
FMPR closely
Active-set convergence with convergence determined by relative difference in loss
Implemented active-set doubling to avoid having to iterate over all
coordinates when checking convergence.
WIP: convergence is broken when gamma>0, active set method needs a final iteration over all coordinates
Fixed bug in initialisation of xcaches, doubled cache size to 2^28