add width and shift params of the gaussian distribution in the down-shift mode of msImpute to provide more control over the shape of the distribution when observed peptides have high average expression and missing is group-specific.
Users can now specify the rank of the model to fit by msImpute
Added mspip for identification transfer between runs using Maxquant results (Beta phase only)
Added evidenceToMatrix which creates limma compatible objects from MaxQuant evidence table
update doc for msImpute
fix typo in msImpute man page
Bug fix in the internal function l2bary
selectFeatures and msImpute now use information theoretic approaches
to find informative features for MAR/MNAR diagnosis and estimation of optimal rank, respectively.
lambda in msImpute is now estimated from the data, using the bayesian interpretation of
this shrinkage operator.
msImpute can be run in three modes: "v1" is the original implementation of softImpute-als
algorithm, "v2" is the enhanced low-rank estimation implemented in this version update, "v2-mnar"
is adaptation of low-rank models for MNAR data. More details about methods in documentation.
Submitted to Bioconductor