Error in NMF estimation
0
0
Entering edit mode
TRASA • 0
@trasa-17881
Last seen 3.3 years ago

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
MutationalPatterns NMF • 598 views
ADD COMMENT

Login before adding your answer.

Traffic: 232 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6