The SomaticSignatures package offers the framework for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.
Home Page: http://bioconductor.org/packages/SomaticSignatures/
License: MIT License
The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.
For details about usage, installation and methodology, please refer to the SomaticSignatures package page in the Bioconductor repository.
Hi,
when I used
gof_nmf = assessNumberSignatures(sca_mm, n_sigs, nReplicates = 5),
I got errors
Error in (function (x) :
unused arguments (model = list(model = "NMFstd", rank = 2, target = 0), method = "random")
Would you please help me？
my sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 20 (Heisenbug)
Matrix products: default
BLAS: /home/users/xu/local/lib64/R/lib/libRblas.so
LAPACK: /home/users/xu/local/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
[2] BSgenome_1.44.0
[3] rtracklayer_1.36.2
[4] ggplot2_2.2.1
[5] SomaticCancerAlterations_1.12.0
[6] SomaticSignatures_2.12.0
[7] VariantAnnotation_1.22.0
[8] Rsamtools_1.28.0
[9] Biostrings_2.44.0
[10] XVector_0.16.0
[11] SummarizedExperiment_1.6.1
[12] DelayedArray_0.2.4
[13] matrixStats_0.52.2
[14] Biobase_2.36.2
[15] GenomicRanges_1.28.2
[16] GenomeInfoDb_1.12.0
[17] IRanges_2.10.1
[18] S4Vectors_0.14.1
[19] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.8.0 bitops_1.0-6
[3] doParallel_1.0.10 RColorBrewer_1.1-2
[5] httr_1.2.1 tools_3.4.0
[7] backports_1.0.5 R6_2.2.1
[9] rpart_4.1-11 Hmisc_4.0-3
[11] DBI_0.6-1 lazyeval_0.2.0
[13] colorspace_1.3-2 nnet_7.3-12
[15] gridExtra_2.2.1 GGally_1.3.0
[17] compiler_3.4.0 graph_1.54.0
[19] htmlTable_1.9 exomeCopy_1.22.0
[21] pkgmaker_0.22 ggbio_1.24.0
[23] scales_0.4.1 checkmate_1.8.2
[25] NMF_0.20.6 proxy_0.4-17
[27] RBGL_1.52.0 stringr_1.2.0
[29] digest_0.6.12 foreign_0.8-68
[31] base64enc_0.1-3 dichromat_2.0-0
[33] htmltools_0.3.6 ensembldb_2.0.1
[35] htmlwidgets_0.8 rlang_0.1.1
[37] RSQLite_1.1-2 BiocInstaller_1.26.0
[39] shiny_1.0.3 BiocParallel_1.10.1
[41] acepack_1.4.1 RCurl_1.95-4.8
[43] magrittr_1.5 GenomeInfoDbData_0.99.0
[45] Formula_1.2-1 Matrix_1.2-10
[47] Rcpp_0.12.11 munsell_0.4.3
[49] stringi_1.1.5 yaml_2.1.14
[51] zlibbioc_1.22.0 plyr_1.8.4
[53] AnnotationHub_2.8.1 grid_3.4.0
[55] lattice_0.20-35 splines_3.4.0
[57] GenomicFeatures_1.28.0 knitr_1.16
[59] rngtools_1.2.4 reshape2_1.4.2
[61] codetools_0.2-15 biomaRt_2.32.0
[63] XML_3.98-1.7 biovizBase_1.24.0
[65] latticeExtra_0.6-28 pcaMethods_1.68.0
[67] data.table_1.10.4 httpuv_1.3.3
[69] foreach_1.4.3 gtable_0.2.0
[71] reshape_0.8.6 gridBase_0.4-7
[73] mime_0.5 xtable_1.8-2
[75] AnnotationFilter_1.0.0 survival_2.41-3
[77] tibble_1.3.1 OrganismDbi_1.18.0
[79] iterators_1.0.8 GenomicAlignments_1.12.1
[81] AnnotationDbi_1.38.0 registry_0.3
[83] memoise_1.1.0 cluster_2.0.6
[85] interactiveDisplayBase_1.14.0
... (solved)
Hello,
The tool is really interersting. I have a question. I want to normalize my whole exome samples to the genome level. I used KmerFrequency of your package. I followed the same example as listed in the vignette. But I am not sure what value to add for n. As the default seems to be n=1e4. Can you please tell how can I decide the "n" value ?
Hi, author,
which way I should use , pmsignature or SomaticSignatures ??
Expecting your answer!
Best wishes!
Hi,
Thanks for a great package!
As I read in many articles, there are several databases with already identified mutational signatures (for example, COSMIC database, http://cancer.sanger.ac.uk/cosmic/signatures).
And how can I compute a matrix H (contribution of each signature to the alterations present in each sample) with already specified matrices M (motif matrix) and W (signatures matrix)?
And I think it would be a good improvement to add such method to the package SomaticSignatures.
Thanks for an advice,
Sergey Kazakov, ITMO University.
Hi,
First of all thank you for creating a stable and useful software for mutation signature analysis. I spent more than a week dealing other softwares loading vcf file step. so thank you!
I would like to compare mutational signature of TF proximity mutations vs (genome - TF binding proximity regions). So I have to make a proper normalisation for the sequence context.
Can I solve my problem with 4.8 Extension: Normalization of Sequence Motif Frequencies. I am thinking about giving my TF binding areas as a bed input instead of hg19 gene exons like you have explained in the introduction part.
Any comment will be very useful.
Best regards,
Tunc.
Would it be too much trouble to add some info here on github what I should expect your algorithm to do?
What does it use as input? I would like to just feed it VCF files.
What do I get as output?
Dear Julian,
Thank you for creating SomaticSignature, it is helping me a lot through my
masters degree.
I have a question about the package. so in "Deciphering signature of
mutational processes operative in human cancer paper", they mention about a
minimum number of mutations required for accurate prediction. I see that
you have not mention about a limiting parameter about this subject. Is
there a number which I should be cautious ?
Right now, I am comparing DHS regions mutation signature versus rest of the
mutations' signature in prostate cancer. My number in one of the samples
seems not too high and there I am having concerns about If the signature
that I see is a false positive or a noise.
Any idea would be very helpful,
Best regards,
Tunc.
Hi,
This is not a problem with this software rather my confusion
I have a list of .vcf files from WGS contains called SNV and indels. I have extracted information from them like below
> head(mutations)
sampleID chr pos ref mut
1 t_005 1 928006 G A
2 t_005 1 1649842 G T
3 t_005 1 2020408 G A
4 t_005 1 2031677 T A
5 t_005 1 2901878 G A
6 t_005 1 3039338 G A
>
I want to make VRanges object from my vcf files or the information I extracted from .vcf files, because I need to find signature in my WGS samples, could you please help me?
Thanks a lot in advance
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