\name{NEWS}
\title{News for package \pkg{GeneNMF}}
\encoding{UTF-8}

\section{Version 0.9.2}{
  New in this version:
  \itemize{
    \item Fix issue with running multiNMF on a sigle sample
    \item Improved definition of cumulative weight for genes in MP
    \item Update category -> collection for runGSEA
    \item Replace deprecated 'slot' calls
    \item Easier implementation for custom annotation colors (as named vectors)
  }
}

\section{Version 0.8.0}{
  New in this version:
  \itemize{
    \item Compatibility with RcppML >= 0.5.6 (currently not on CRAN)
  }
}

\section{Version 0.7.0}{
  New in this version:
  \itemize{
    \item The function 'getMetaPrograms()' now returns also a matrix of "metaprogram composition", in terms of how many individual programs from each sample contributed to defining the MP. This is stored in the 'metaprograms.composition' slot of the resulting object
    \item The function 'runGSEA()' now allows running gene set enrichment against a custom DB of signatures
    \item Check that parameter 'k' is an integer >=2
  }
}

\section{Version 0.6.2}{
  New in this version:
  \itemize{
    \item Automatic downsample of the gene program similarity heatmap (plotMetaPrograms() function). It avoids overloading the graphics device when running GeneNMF with many samples. See the 'downsample' parameter in plotMetaPrograms().
    \item New function 'dropMetaPrograms()' to remove MPs from GeneNMF results. 
  }
}

\section{Version 0.6.0}{
  New in this version:
  \itemize{
    \item We updated how meta-programs (MPs) are calculated from individual programs. Instead of extracting gene sets for each program and then calculating a consensus, we keep the full vector of gene weights and calculate cosine similarities between the vectors. Consensus gene weights are then calculated as the average over all programs in a MP. 
    \item To impose sparsity in the decomposition, we include a `specificity.weight` parameter, which is used to re-normalize NMF loadings based on how specific a gene is for a given program. 
    \item To determine the number of genes to be included in a MP, we calculate the cumulative distribution for the gene weights in a given MP. Only genes that cumulatively explain up to a fraction of the total weight (`weight.explained` parameter) are included in the MP gene set.
    \item The definition and default of `min.confidence` has changed. The confidence of a gene in a given MP is calculated as the fraction of programs in which the gene has been determined to be part of the invidual program (using `weight.explained=0.8`).
    \item The parameter `nprograms` in the function `getMetaPrograms()` has been renamed to `nMP`, to avoid confusion
    \item New defaults: expression matrices are now by default not scaled or centered (the behavior can be altered using the `scale` and `center` parameters)
  }
}

\section{Version 0.4.0}{
  \itemize{
    \item First stable version
  }
}
