Estimatesignature

[ghost]

hello, while running this command I am getting this error. Thank you

luad.tnm = trinucleotideMatrix(maf = subsetMaf(luad, genes = "KRAS",), prefix = 'chr', add = TRUE, ref_genome = "BSgenome.Hsapiens.UCSC.hg19")
-Extracting 5' and 3' adjacent bases
-Extracting +/- 20bp around mutated bases for background C>T estimation
-Estimating APOBEC enrichment scores
--Performing one-way Fisher's test for APOBEC enrichment
---APOBEC related mutations are enriched in 4.348 % of samples (APOBEC enrichment score > 2 ; 2 of 46 samples)
-Creating mutation matrix
--matrix of dimension 157x96
luad.sign = estimateSignatures(mat = luad.tnm, nTry = 6)
-Found zero mutations for conversions:
A[C>A]A
A[C>A]G
A[C>A]T
C[C>A]C
C[C>A]G
C[C>A]T
G[C>A]A
G[C>A]C
G[C>A]G
G[C>A]T
T[C>A]C
T[C>A]G
T[C>A]T
A[C>G]A
A[C>G]G
A[C>G]T
C[C>G]A
C[C>G]C
C[C>G]G
C[C>G]T
G[C>G]A
G[C>G]C
G[C>G]G
T[C>G]C
T[C>G]G
T[C>G]T
A[C>T]A
A[C>T]G
A[C>T]T
C[C>T]C
C[C>T]G
C[C>T]T
G[C>T]A
G[C>T]G
G[C>T]T
T[C>T]A
T[C>T]C
T[C>T]G
T[C>T]T
A[T>A]A
A[T>A]G
A[T>A]T
C[T>A]A
C[T>A]C
C[T>A]G
G[T>A]A
G[T>A]C
G[T>A]G
G[T>A]T
T[T>A]C
T[T>A]T
A[T>C]A
A[T>C]C
A[T>C]G
A[T>C]T
C[T>C]A
C[T>C]C
C[T>C]G
C[T>C]T
G[T>C]A
G[T>C]C
G[T>C]G
G[T>C]T
T[T>C]A
T[T>C]C
T[T>C]G
T[T>C]T
A[T>G]A
A[T>G]C
A[T>G]G
A[T>G]T
C[T>G]A
C[T>G]C
C[T>G]G
C[T>G]T
G[T>G]A
G[T>G]C
G[T>G]G
G[T>G]T
T[T>G]A
T[T>G]C
T[T>G]G
T[T>G]T
-Running NMF for 6 ranks
Compute NMF rank= 2 ... Timing stopped at: 2.91 0.03 3.97
ERROR
Compute NMF rank= 3 ... Timing stopped at: 2.03 0 3.13
ERROR
Compute NMF rank= 4 ... Timing stopped at: 1.83 0.03 2.83
ERROR
Compute NMF rank= 5 ... Timing stopped at: 2.88 0.02 4.42
ERROR
Compute NMF rank= 6 ... Timing stopped at: 2.94 0.04 4.74
ERROR
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: NMF::nmf - Input matrix x contains at least one null or NA-filled row.
  -VCF to MAF conversion? #2 [r=3] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: NMF::nmf - Input matrix x contains at least one null or NA-filled row.
  -feature request: rainfall plot #3 [r=4] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: NMF::nmf - Input matrix x contains at least one null or NA-filled row.
  -Dockerizeit #4 [r=5] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: NMF::nmf - Input matrix x contains at least one null or NA-filled row.
  -CNV/RNAseq data into oncoplot #5 [r=6] -> NMF::nmf - 10/10 fit(s) threw an error.

Error(s) thrown:

• run writeup/DOI #1: NMF::nmf - Input matrix x contains at least one null or NA-filled ro```r

**Session info**
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] dplyr_1.0.1                       doParallel_1.0.15                
 [3] iterators_1.0.12                  foreach_1.5.0                    
 [5] NMF_0.23.0                        Biobase_2.48.0                   
 [7] cluster_2.1.0                     rngtools_1.5                     
 [9] pkgmaker_0.31.1                   registry_0.5-1                   
[11] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.56.0                  
[13] rtracklayer_1.48.0                Biostrings_2.56.0                
[15] XVector_0.28.0                    GenomicRanges_1.40.0             
[17] GenomeInfoDb_1.24.2               IRanges_2.22.2                   
[19] S4Vectors_0.26.1                  BiocGenerics_0.34.0              
[21] maftools_2.4.05                  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                  lattice_0.20-41            
 [3] Rsamtools_2.4.0             assertthat_0.2.1           
 [5] digest_0.6.25               gridBase_0.4-7             
 [7] R6_2.4.1                    plyr_1.8.6                 
 [9] TCGAmutations_0.3.0         ggplot2_3.3.2              
[11] pillar_1.4.6                zlibbioc_1.34.0            
[13] rlang_0.4.7                 rstudioapi_0.11            
[15] data.table_1.13.0           Matrix_1.2-18              
[17] splines_4.0.2               BiocParallel_1.22.0        
[19] stringr_1.4.0               RCurl_1.98-1.2             
[21] munsell_0.5.0               DelayedArray_0.14.1        
[23] compiler_4.0.2              pkgconfig_2.0.3            
[25] tidyselect_1.1.0            SummarizedExperiment_1.18.2
[27] tibble_3.0.3                GenomeInfoDbData_1.2.3     
[29] codetools_0.2-16            matrixStats_0.56.0         
[31] XML_3.99-0.5                crayon_1.3.4               
[33] withr_2.2.0                 GenomicAlignments_1.24.0   
[35] bitops_1.0-6                grid_4.0.2                 
[37] xtable_1.8-4                gtable_0.3.0               
[39] lifecycle_0.2.0             magrittr_1.5               
[41] scales_1.1.1                bibtex_0.4.2.2             
[43] stringi_1.4.6               reshape2_1.4.4             
[45] ellipsis_0.3.1              vctrs_0.3.2                
[47] generics_0.0.2              RColorBrewer_1.1-2         
[49] tools_4.0.2                 glue_1.4.1                 
[51] purrr_0.3.4                 survival_3.1-12            
[53] colorspace_1.4-1            BiocManager_1.30.10   

[PoisonAlien]

Hi,
Estimatesignature or any sort of signature analysis can not be done on a single gene level (it seems you;re sub-setting for KRAS). Mutation load is too low to run NMF. This also why you're getting zero counts warning.

[ghost]

Thank you!
Is there any other way to get around this issue?

[PoisonAlien]

Try same command with pConstant = 0.01. It will add small positive constant value to avoid zeros. But be very careful to interpret the results.