Hi,

I'm trying to run nmfSignatures function and I've got the following error

> sigs_trio_nmf <- nmfSignatures(vr_mm_trio, n_sigs, nmfSignatures)
Error in 1:r : NA/NaN argument
Timing stopped at: 0.603 0.001 0.603

I suppose that this is caused because my matrix have some 0's. The example from the html tutorial works fine and the same matrix run fine in previous releases of SomaticSignatures. You can obtain the matrix from here

I'm using the package version 2.2.1 and R version 3.1.1.

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
 [2] GenomicFeatures_1.18.1                 
 [3] gplots_2.14.2                          
 [4] gtools_3.4.1                           
 [5] BSgenome.Hsapiens.UCSC.hg19_1.3.99     
 [6] BSgenome_1.34.0                        
 [7] rtracklayer_1.26.1                     
 [8] org.Hs.eg.db_3.0.0                     
 [9] RSQLite_1.0.0                          
[10] DBI_0.3.1                              
[11] AnnotationDbi_1.28.0                   
[12] SomaticCancerAlterations_1.1.1         
[13] stringr_0.6.2                          
[14] SomaticSignatures_2.2.1                
[15] Biobase_2.26.0                         
[16] VariantAnnotation_1.12.2               
[17] Rsamtools_1.18.1                       
[18] Biostrings_2.34.0                      
[19] XVector_0.6.0                          
[20] GenomicRanges_1.18.1                   
[21] GenomeInfoDb_1.2.0                     
[22] IRanges_2.0.0                          
[23] S4Vectors_0.4.0                        
[24] BiocGenerics_0.12.0                    
[25] reshape_0.8.5                          
[26] gridExtra_0.9.1                        
[27] scales_0.2.4                           
[28] xtable_1.7-4                           
[29] wesanderson_0.3                        
[30] RColorBrewer_1.0-5                     
[31] ggplot2_1.0.0                          

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         base64enc_0.1-2         BatchJobs_1.4          
 [4] BBmisc_1.7              BiocParallel_1.0.0      biomaRt_2.22.0         
 [7] biovizBase_1.14.0       bitops_1.0-6            brew_1.0-6             
[10] caTools_1.17.1          checkmate_1.5.0         cluster_1.15.3         
[13] codetools_0.2-9         colorspace_1.2-4        dichromat_2.0-0        
[16] digest_0.6.4            doParallel_1.0.8        exomeCopy_1.12.0       
[19] fail_1.2                foreach_1.4.2           foreign_0.8-61         
[22] Formula_1.1-2           gdata_2.13.3            GenomicAlignments_1.2.0
[25] GGally_0.4.8            ggbio_1.14.0            graph_1.44.0           
[28] gridBase_0.4-7          gtable_0.1.2            Hmisc_3.14-5           
[31] iterators_1.0.7         KernSmooth_2.23-13      labeling_0.3           
[34] lattice_0.20-29         latticeExtra_0.6-26     MASS_7.3-35            
[37] munsell_0.4.2           NMF_0.20.5              nnet_7.3-8             
[40] OrganismDbi_1.8.0       pcaMethods_1.56.0       pkgmaker_0.22          
[43] plyr_1.8.1              proto_0.3-10            proxy_0.4-13           
[46] RBGL_1.42.0             Rcpp_0.11.3             RCurl_1.95-4.3         
[49] registry_0.2            reshape2_1.4            rngtools_1.2.4         
[52] rpart_4.1-8             sendmailR_1.2-1         splines_3.1.1          
[55] survival_2.37-7         tools_3.1.1             XML_3.98-1.1           
[58] zlibbioc_1.12.0        

The problem here is that you use the function <font face="monospace">nmfSignatures in two different contexts.  I guess that you have been using the SomaticSignatures versions 1.*.* already in the last release, and there was somehow a leftover from transitioning to the new synthax.  If you have a look at the vignette, your line better looks like this:</font>

sigs_trio_nmf <- identifySignatures(vr_mm_trio, n_sigs, decomposition = nmfSignatures)

To explain a bit: identifySignatures is the high-level function, nmfSignatures is the decomposition method that you want to apply (here, you can plug in the function that you like most). In your example, you used the decomposition function twice - which ended up apply the decomposition on itself.

I can see where the confusion comes from. I'll think of a good way to avoid this in future versions, and release a fix for until next week.

You're right, problem solved. Sorry for the confusion with the previous version. You still want a have the motifMatrix with normalize = FALSE?

Thanks a lot