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
Thank you! I tried it only with one sample to do a quick test of the package. I added the rest of them and run perfectly.
Hi Renan,
I tried to use SigneR 1.6.1 on one sample and got the message described above. Is that the expected behavior on that version?
If so, is there a way to "enforce" signeR to be suitable to one sample? What will be the results if I am duplicating the column with my sample so that the vcf will have "two" samples which are exactly the same?
Thank you in advance for you help,
Dana