decompose matrix into n signatures. Default NULL. Tries to predict best value for n by running NMF on a range of values and chooses based on cophenetic correlation coefficient.
nTry
tries upto this number of signatures before choosing best n. Default 6.
plotBestFitRes
plots consensus heatmap for range of values tried. Default FALSE
parallel
calls to .opt argument of nmf. e.g, 'P4' for using 4 cores. See note on nmf for MAC users.
Value
a list with decomposed scaled signatures, signature contributions in each sample and a correlatoon table against validated signatures.
Details
This function decomposes a non-negative matrix into n signatures.
Extracted signatures are compared against 21 experimentally validated signatures by calculating correlation coefficient. See http://www.nature.com/nature/journal/v500/n7463/fig_tab/nature12477_F2.html for details.