could not find function "get_known_signatures"
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anton.kratz ▴ 60
@antonkratz-8836
Last seen 7 weeks ago
United States, San Diego, UCSD

I am new to MutationalPatterns. I am trying to follow the tutorial and do signature refitting. The problem is that could not find function "get_known_signatures":

Code should be placed in three backticks as shown below

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

[Workspace loaded from ~/.RData]

> library(MutationalPatterns)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
    which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 7/8
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: ‘NMF’

The following object is masked from ‘package:S4Vectors’:

    nrun

> get_known_signatures()
Error in get_known_signatures() : 
  could not find function "get_known_signatures"
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] MutationalPatterns_1.12.0 NMF_0.25                  Biobase_2.46.0           
 [4] cluster_2.1.0             rngtools_1.5.2            registry_0.5-1           
 [7] GenomicRanges_1.38.0      GenomeInfoDb_1.22.1       IRanges_2.20.2           
[10] S4Vectors_0.24.4          BiocGenerics_0.32.0      

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                matrixStats_0.63.0         
 [3] bit64_4.0.5                 doParallel_1.0.17          
 [5] RColorBrewer_1.1-3          progress_1.2.2             
 [7] httr_1.4.4                  tools_3.6.3                
 [9] utf8_1.2.2                  R6_2.5.1                   
[11] DBI_1.1.3                   colorspace_2.0-3           
[13] tidyselect_1.2.0            prettyunits_1.1.1          
[15] bit_4.0.5                   curl_4.3.3                 
[17] compiler_3.6.3              cli_3.4.1                  
[19] DelayedArray_0.12.3         ggdendro_0.1.23            
[21] rtracklayer_1.46.0          scales_1.2.1               
[23] askpass_1.1                 rappdirs_0.3.3             
[25] stringr_1.5.0               digest_0.6.30              
[27] Rsamtools_2.2.3             XVector_0.26.0             
[29] pkgconfig_2.0.3             dbplyr_2.2.1               
[31] fastmap_1.1.0               BSgenome_1.54.0            
[33] rlang_1.0.6                 rstudioapi_0.14            
[35] RSQLite_2.2.0               generics_0.1.3             
[37] BiocParallel_1.20.1         dplyr_1.0.10               
[39] VariantAnnotation_1.32.0    RCurl_1.98-1.9             
[41] magrittr_2.0.3              GenomeInfoDbData_1.2.2     
[43] Matrix_1.2-18               Rcpp_1.0.9                 
[45] munsell_0.5.0               fansi_1.0.3                
[47] lifecycle_1.0.3             stringi_1.7.8              
[49] MASS_7.3-51.5               SummarizedExperiment_1.16.1
[51] zlibbioc_1.32.0             plyr_1.8.8                 
[53] BiocFileCache_1.10.2        grid_3.6.3                 
[55] blob_1.2.3                  crayon_1.5.2               
[57] lattice_0.20-40             Biostrings_2.54.0          
[59] cowplot_1.1.1               GenomicFeatures_1.38.2     
[61] hms_1.1.2                   pillar_1.8.1               
[63] reshape2_1.4.3              codetools_0.2-16           
[65] biomaRt_2.42.1              XML_3.99-0.3               
[67] glue_1.6.2                  BiocManager_1.30.19        
[69] vctrs_0.5.1                 foreach_1.4.8              
[71] gtable_0.3.1                openssl_2.0.5              
[73] assertthat_0.2.1            cachem_1.0.6               
[75] ggplot2_3.4.0               gridBase_0.4-7             
[77] pracma_2.4.2                tibble_3.1.8               
[79] iterators_1.0.12            GenomicAlignments_1.22.1   
[81] AnnotationDbi_1.48.0        memoise_2.0.1              
[83] ellipsis_0.3.2
MutationalPatterns • 125 views
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Version 1.12.0 seems quite old as the latest is 3.7.1, install_github("UMCUGenetics/MutationalPatterns")

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Entering edit mode

The function is available in later versions of MutationalPatterns than the one you are using. It would be best to use a current version of R (4.2.2) and BiocManager::install to get the current release.

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