Hi,

I am using the bioconductor package for first time, following the vignette step by step. I loaded my vcf and bed files, and created the mut and opp matrix without problems, but when running signeR() I get this:

> signatures <- signeR(M=mut, Opport=opp)

Evaluating models with the number of signatures ranging from 1 to 0, please be patient.
Error in seq.default(liminf, limsup, by = step) : 
  wrong sign in 'by' argument

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.42.0                   rtracklayer_1.34.1                VariantAnnotation_1.20.2          Rsamtools_1.24.0                 
 [6] Biostrings_2.40.2                 XVector_0.12.1                    SummarizedExperiment_1.4.0        GenomicRanges_1.26.1              GenomeInfoDb_1.8.7               
[11] IRanges_2.8.1                     S4Vectors_0.12.1                  signeR_1.0.0                      Biobase_2.32.0                    BiocGenerics_0.20.0              
[16] BiocInstaller_1.24.0              rgl_0.96.0                        corrplot_0.77                     reshape2_1.4.2                    lattice_0.20-34                  
[21] ggplot2_2.2.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8              class_7.3-14             assertthat_0.1           digest_0.6.10            foreach_1.4.3            gridBase_0.4-7           mime_0.5                
 [8] R6_2.2.0                 plyr_1.8.4               RSQLite_1.1              zlibbioc_1.18.0          GenomicFeatures_1.26.0   lazyeval_0.2.0           nloptr_1.0.4            
[15] Matrix_1.2-7.1           BiocParallel_1.8.1       stringr_1.1.0            htmlwidgets_0.8          RCurl_1.95-4.8           biomaRt_2.30.0           munsell_0.4.3           
[22] shiny_0.14.2             httpuv_1.3.3             pkgmaker_0.22            htmltools_0.3.5          tibble_1.2               codetools_0.2-15         XML_3.98-1.5            
[29] GenomicAlignments_1.10.0 bitops_1.0-6             grid_3.3.2               jsonlite_1.1             xtable_1.8-2             gtable_0.2.0             registry_0.3            
[36] DBI_0.5-1                magrittr_1.5             scales_0.4.1             stringi_1.1.2            doParallel_1.0.10        RColorBrewer_1.1-2       NMF_0.20.6              
[43] iterators_1.0.8          tools_3.3.2              PMCMR_4.1                rngtools_1.2.4           AnnotationDbi_1.34.4     colorspace_1.3-1         cluster_2.0.5           
[50] memoise_1.0.0            knitr_1.15.1 

Any clue why this is happening?

Thank you for your help,

Miguel

Hello Miguel,

could you post the dimensions of the mut and opp matrices ? how many samples do you have ?

signeR will dynamically adjust the number of signatures tested depending on the input matrix dimensions, however its not possible to run the algorithm for a single sample, sorry, in future updates we will have a clearer error message.