Question: Error in NMF estimation
0
gravatar for TRASA
5 months ago by
TRASA0
TRASA0 wrote:

Hi

I would like to perform de novo mutational signature extraction. I am trying to follow the vignette of the MutationalPattern package. I managed to create the matrix for my samples. However, I encounter problems when I try to estiamte the number of mutational signatures in my samples. Here my code and corresponding errors:

estimate<- nmf(mut_mat, rank=2:5, method="brunet", nrun=30, seed=123456)

Timing stopped at: 1.743 0.306 1.875
Timing stopped at: 1.732 0.309 1.881
Timing stopped at: 1.979 0.346 2.183
Timing stopped at: 1.765 0.309 1.899
Error in (function (...)  : All the runs produced an error:
    -#1 [r=2] -> NMF::nmf - 30/30 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list("NMFstd", 2, 0), method = "random")
    -#2 [r=3] -> NMF::nmf - 30/30 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list("NMFstd", 3, 0), method = "random")
    -#3 [r=4] -> NMF::nmf - 30/30 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list("NMFstd", 4, 0), method = "random")
    -#4 [r=5] -> NMF::nmf - 30/30 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list("NMFstd", 5, 0), method = "random")

Has anybody encountered a similar problem and solved it?

Thanks for your help.

Below you find sessionInfo:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] signeR_1.8.0                      doParallel_1.0.14                 iterators_1.0.10                 
 [4] foreach_1.4.4                     VariantAnnotation_1.28.13         Rsamtools_1.34.1                 
 [7] SummarizedExperiment_1.12.0       DelayedArray_0.8.0                BiocParallel_1.16.6              
[10] matrixStats_0.54.0                readxl_1.3.1                      BSgenome.Hsapiens.UCSC.hg38_1.4.1
[13] BSgenome_1.50.0                   rtracklayer_1.42.2                Biostrings_2.50.2                
[16] XVector_0.22.0                    MutationalPatterns_1.8.0          NMF_0.21.0                       
[19] bigmemory_4.5.33                  Biobase_2.42.0                    cluster_2.0.9                    
[22] rngtools_1.3.1                    pkgmaker_0.27                     registry_0.5-1                   
[25] GenomicRanges_1.34.0              GenomeInfoDb_1.18.2               IRanges_2.16.0                   
[28] S4Vectors_0.20.1                  BiocGenerics_0.28.0              

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       progress_1.2.2          
 [5] httr_1.4.0               tools_3.5.1              R6_2.4.0                 DBI_1.0.0               
 [9] lazyeval_0.2.2           colorspace_1.4-1         withr_2.1.2              tidyselect_0.2.5        
[13] prettyunits_1.0.2        PMCMR_4.3                bit_1.1-14               compiler_3.5.1          
[17] ggdendro_0.1-20          scales_1.0.0             stringr_1.4.0            digest_0.6.18           
[21] pkgconfig_2.0.2          bibtex_0.4.2             rlang_0.3.4              rstudioapi_0.10         
[25] RSQLite_2.1.1            dplyr_0.8.1              RCurl_1.95-4.12          magrittr_1.5            
[29] GenomeInfoDbData_1.2.0   Matrix_1.2-17            Rcpp_1.0.1               munsell_0.5.0           
[33] stringi_1.4.3            yaml_2.2.0               MASS_7.3-51.4            zlibbioc_1.28.0         
[37] plyr_1.8.4               grid_3.5.1               blob_1.1.1               bigmemory.sri_0.1.3     
[41] crayon_1.3.4             lattice_0.20-38          cowplot_0.9.4            GenomicFeatures_1.34.8  
[45] hms_0.4.2                pillar_1.4.0             reshape2_1.4.3           codetools_0.2-16        
[49] biomaRt_2.38.0           XML_3.98-1.19            glue_1.3.1               BiocManager_1.30.4      
[53] nloptr_1.2.1             cellranger_1.1.0         gtable_0.3.0             purrr_0.3.2             
[57] assertthat_0.2.1         ggplot2_3.1.1            gridBase_0.4-7           xtable_1.8-4            
[61] pracma_2.2.5             class_7.3-15             tibble_2.1.1             GenomicAlignments_1.18.1
[65] AnnotationDbi_1.44.0     memoise_1.1.0
nmf mutationalpatterns • 74 views
ADD COMMENTlink written 5 months ago by TRASA0
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