GeneNMF v0.6.2

New in this version:

• Automatic downsampling 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().
• New function 'dropMetaPrograms()' to remove MPs from GeneNMF results. It allows e.g. to plot the MP similarity heatmap without a subset of meta-programs.

GeneNMF v0.6.0

New in this version:

• 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.
• 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.
• 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.
• 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).
• The parameter nprograms in the function getMetaPrograms() has been renamed to nMP, to avoid confusion
• New defaults: expression matrices are now by default not scaled or centered (the behavior can be altered using the scale and center parameters)

GeneNMF v0.4.0

GeneNMF v0.4.0

First stable release, available from CRAN.