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friend1ws / pmsignature

R package for extracting mutation signatures from a list of somatic mutations
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Signature plot not available for Kth (last) signature #15

Open BrunoGrandePhD opened 8 years ago

BrunoGrandePhD commented 8 years ago

Hello Yuichi. I've been trying out pmsignature. Thanks for the package!

I just wanted to report an apparent bug that prevents the visualization of the Kth (last) mutation signature. After following the instructions in the README file, I ran into an error (see below) while running visPMSignature for the third (last) signature when K in getPMSignature was set to 3. 

> visPMSignature(pm_sigs, 3)
Error in object@signatureFeatureDistribution[sinInd, , ] : 
  subscript out of bounds

I tried the same with K set to 4 and the fourth signature wasn't available, but the third now was available. Can you reproduce this issue with version 0.2.0 on GitHub (4b09c62)? Thanks.

See below for my session information. 

> devtools::session_info()
Session info -------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.2.2 (2015-08-14)
 system   x86_64, darwin13.4.0        
 ui       RStudio (0.99.893)          
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Vancouver           
 date     2016-03-26                  

Packages -----------------------------------------------------------------------------------------------------
 package                           * version  date       source                                
 acepack                             1.3-3.3  2014-11-24 CRAN (R 3.2.0)                        
 AnnotationDbi                       1.32.3   2015-12-24 Bioconductor                          
 assertthat                          0.1      2013-12-06 CRAN (R 3.2.0)                        
 Biobase                           * 2.30.0   2015-10-14 Bioconductor                          
 BiocGenerics                      * 0.16.1   2015-11-06 Bioconductor                          
 BiocInstaller                     * 1.20.1   2015-11-18 Bioconductor                          
 BiocParallel                        1.4.3    2015-12-17 Bioconductor                          
 biomaRt                             2.26.1   2015-11-23 Bioconductor                          
 Biostrings                        * 2.38.4   2016-02-09 Bioconductor                          
 biovizBase                          1.18.0   2015-10-14 Bioconductor                          
 bitops                              1.0-6    2013-08-17 CRAN (R 3.2.0)                        
 BSgenome                          * 1.38.0   2015-10-14 Bioconductor                          
 BSgenome.Hsapiens.UCSC.hg19         1.4.0    2016-03-26 Bioconductor                          
 BSgenome.Hsapiens.UCSC.hg38       * 1.4.1    2016-03-20 Bioconductor                          
 cluster                             2.0.3    2015-07-21 CRAN (R 3.2.2)                        
 codetools                           0.2-14   2015-07-15 CRAN (R 3.2.2)                        
 colorspace                          1.2-6    2015-03-11 CRAN (R 3.2.0)                        
 cowplot                           * 0.6.1    2016-03-06 CRAN (R 3.2.4)                        
 curl                                0.9.6    2016-02-17 CRAN (R 3.2.3)                        
 DBI                                 0.3.1    2014-09-24 CRAN (R 3.2.0)                        
 devtools                          * 1.10.0   2016-01-23 CRAN (R 3.2.3)                        
 dichromat                           2.0-0    2013-01-24 CRAN (R 3.2.0)                        
 digest                              0.6.9    2016-01-08 CRAN (R 3.2.3)                        
 doParallel                          1.0.10   2015-10-14 CRAN (R 3.2.0)                        
 dplyr                             * 0.4.3    2015-09-01 CRAN (R 3.2.0)                        
 evaluate                            0.8.3    2016-03-05 CRAN (R 3.2.4)                        
 FField                              0.1.0    2013-06-28 CRAN (R 3.2.0)                        
 foreach                             1.4.3    2015-10-13 CRAN (R 3.2.0)                        
 foreign                             0.8-66   2015-08-19 CRAN (R 3.2.0)                        
 formatR                             1.3      2016-03-05 CRAN (R 3.2.4)                        
 Formula                             1.2-1    2015-04-07 CRAN (R 3.2.0)                        
 futile.logger                       1.4.1    2015-04-20 CRAN (R 3.2.0)                        
 futile.options                      1.0.0    2010-04-06 CRAN (R 3.2.0)                        
 GenomeInfoDb                      * 1.6.3    2016-01-26 Bioconductor                          
 GenomicAlignments                   1.6.3    2016-01-06 Bioconductor                          
 GenomicFeatures                     1.22.13  2016-02-11 Bioconductor                          
 GenomicRanges                     * 1.22.4   2016-01-30 Bioconductor                          
 GenVisR                           * 0.99.20  2016-03-20 Github (griffithlab/GenVisR@afbd169)  
 GGally                              1.0.1    2016-01-14 CRAN (R 3.2.3)                        
 ggbio                               1.18.5   2016-02-13 Bioconductor                          
 ggdendro                          * 0.1-18   2016-02-25 CRAN (R 3.2.3)                        
 ggplot2                           * 2.1.0    2016-03-01 CRAN (R 3.2.4)                        
 ggvis                             * 0.4.2    2015-06-06 CRAN (R 3.2.0)                        
 git2r                               0.14.0   2016-03-13 CRAN (R 3.2.4)                        
 graph                               1.48.0   2015-10-14 Bioconductor                          
 gridBase                            0.4-7    2014-02-24 CRAN (R 3.2.0)                        
 gridExtra                           2.2.1    2016-02-29 CRAN (R 3.2.4)                        
 gtable                              0.2.0    2016-02-26 CRAN (R 3.2.3)                        
 gtools                              3.5.0    2015-05-29 CRAN (R 3.2.0)                        
 highr                               0.5.1    2015-09-18 CRAN (R 3.2.0)                        
 Hmisc                               3.17-2   2016-02-21 CRAN (R 3.2.3)                        
 htmltools                           0.3.5    2016-03-21 CRAN (R 3.2.4)                        
 httpuv                              1.3.3    2015-08-04 CRAN (R 3.2.0)                        
 httr                                1.1.0    2016-01-28 CRAN (R 3.2.3)                        
 IRanges                           * 2.4.8    2016-02-26 Bioconductor                          
 iterators                           1.0.8    2015-10-13 CRAN (R 3.2.0)                        
 jsonlite                            0.9.19   2015-11-28 CRAN (R 3.2.2)                        
 knitr                             * 1.12.3   2016-01-22 CRAN (R 3.2.3)                        
 labeling                            0.3      2014-08-23 CRAN (R 3.2.0)                        
 lambda.r                            1.1.7    2015-03-20 CRAN (R 3.2.0)                        
 lattice                             0.20-33  2015-07-14 CRAN (R 3.2.2)                        
 latticeExtra                        0.6-28   2016-02-09 CRAN (R 3.2.3)                        
 lazyeval                            0.1.10   2015-01-02 CRAN (R 3.2.0)                        
 magrittr                            1.5      2014-11-22 CRAN (R 3.2.0)                        
 MASS                                7.3-45   2015-11-10 CRAN (R 3.2.2)                        
 memoise                             1.0.0    2016-01-29 CRAN (R 3.2.3)                        
 mime                                0.4      2015-09-03 CRAN (R 3.2.0)                        
 munsell                             0.4.3    2016-02-13 CRAN (R 3.2.3)                        
 NMF                                 0.20.6   2015-05-26 CRAN (R 3.2.0)                        
 nnet                                7.3-12   2016-02-02 CRAN (R 3.2.3)                        
 OrganismDbi                         1.12.1   2015-12-23 Bioconductor                          
 pcaMethods                          1.60.0   2015-10-14 Bioconductor                          
 pkgmaker                            0.22     2014-05-14 CRAN (R 3.2.0)                        
 plyr                                1.8.3    2015-06-12 CRAN (R 3.2.0)                        
 pmsignature                       * 0.2.0    2016-03-27 Github (friend1ws/pmsignature@4b09c62)
 proxy                               0.4-15   2015-07-08 CRAN (R 3.2.0)                        
 R6                                  2.1.2    2016-01-26 CRAN (R 3.2.3)                        
 RBGL                                1.46.0   2015-10-14 Bioconductor                          
 RColorBrewer                      * 1.1-2    2014-12-07 CRAN (R 3.2.0)                        
 Rcpp                                0.12.4   2016-03-26 CRAN (R 3.2.2)                        
 RCurl                               1.95-4.8 2016-03-01 CRAN (R 3.2.4)                        
 readr                             * 0.2.2    2015-10-22 CRAN (R 3.2.0)                        
 registry                            0.3      2015-07-08 CRAN (R 3.2.0)                        
 reshape                             0.8.5    2014-04-23 CRAN (R 3.2.0)                        
 reshape2                            1.4.1    2014-12-06 CRAN (R 3.2.0)                        
 rngtools                            1.2.4    2014-03-06 CRAN (R 3.2.0)                        
 rpart                               4.1-10   2015-06-29 CRAN (R 3.2.2)                        
 Rsamtools                         * 1.22.0   2015-10-14 Bioconductor                          
 rsconnect                           0.4.2    2016-03-20 CRAN (R 3.2.2)                        
 RSQLite                             1.0.0    2014-10-25 CRAN (R 3.2.0)                        
 rtracklayer                       * 1.30.3   2016-03-15 Bioconductor                          
 S4Vectors                         * 0.8.11   2016-01-29 Bioconductor                          
 scales                              0.4.0    2016-02-26 CRAN (R 3.2.3)                        
 shiny                             * 0.13.1   2016-02-17 CRAN (R 3.2.2)                        
 SomaticSignatures                 * 2.6.0    2015-10-14 Bioconductor                          
 stringi                             1.0-1    2015-10-22 CRAN (R 3.2.0)                        
 stringr                             1.0.0    2015-04-30 CRAN (R 3.2.0)                        
 SummarizedExperiment              * 1.0.2    2016-01-01 Bioconductor                          
 survival                            2.38-3   2015-07-02 CRAN (R 3.2.2)                        
 tidyr                             * 0.4.1    2016-02-05 CRAN (R 3.2.3)                        
 TxDb.Hsapiens.UCSC.hg19.knownGene   3.2.2    2016-03-27 Bioconductor                          
 VariantAnnotation                 * 1.16.4   2015-12-09 Bioconductor                          
 viridis                           * 0.3.4    2016-03-12 CRAN (R 3.2.4)                        
 withr                               1.0.1    2016-02-04 CRAN (R 3.2.3)                        
 XML                                 3.98-1.4 2016-03-01 CRAN (R 3.2.4)                        
 xtable                              1.8-2    2016-02-05 CRAN (R 3.2.3)                        
 XVector                           * 0.10.0   2015-10-14 Bioconductor                          
 zlibbioc                            1.16.0   2015-10-14 Bioconductor
friend1ws commented 8 years ago

Hi, thanks for the interest in pmsignature. Did you use the background signature? When using backgroud signature, the last signature becomes the background. While you can view the membership parameter using visMembership function, you cannot visualize the background signature...

Sorry for the confusion, I will soon at least fix the ReadMe.md for more clarity.