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anton.kratz
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@antonkratz-8836
Last seen 8 months ago
Japan, Tokyo, The Systems Biology Insti…
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
Version 1.12.0 seems quite old as the latest is 3.7.1,
install_github("UMCUGenetics/MutationalPatterns")
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.