News for package GeneNMF

Version 0.9.2

New in this version:

• Fix issue with running multiNMF on a sigle sample

• Improved definition of cumulative weight for genes in MP

• Update category -> collection for runGSEA

• Replace deprecated 'slot' calls

• Easier implementation for custom annotation colors (as named vectors)

Version 0.8.0

New in this version:

• Compatibility with RcppML >= 0.5.6 (currently not on CRAN)

Version 0.7.0

New in this version:

• 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

• The function 'runGSEA()' now allows running gene set enrichment against a custom DB of signatures

• Check that parameter 'k' is an integer >=2

Version 0.6.2

New in this version:

• 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().

• New function 'dropMetaPrograms()' to remove MPs from GeneNMF results.

Version 0.6.0

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)

Version 0.4.0

• First stable version