MMR
Mismatch repair signature analysis in C. elegans and ICGC colorectal and stomach cancer data for Meier, Volkova et al. 2017 (subm.).
C. elegans data: contains .RData files with count and design matrices for MMR experiment on C. elegans, raw data available at the NCBI Sequence Read Archive SRA under accession number SRP020555. Requires C. elegans WB235cel genome, instructions in corresponding README file.
ICGC data:
- COAD: data from ICGC DCC portal on colorectal adenocarcinoma, contains donor and sample codes, MSI status, VCF with all variants per sample; requires downloading data from ICGC portal, instructions in corresponding README file.
- STAD: data from ICGC DCC portal on stomach adenocarcinoma, contains donor and sample codes, MSI status, VCF with all variants per sample; requires downloading data from ICGC portal, instructions in corresponding README file.
- profiles_and_decomposition.RData - contains mutation count matrices, signatures, and decomposition over these signatures. All this data is publicly available from ICGC and TCGA CE.
- requires downloading the meta-VCF with precise description of all the mutations in ICGC data, available here under simple_somatic_mutation.aggregated.vcf.gz.
plotting_functions: contains some codes for signature/profile plotting
exome.RData - contains pre-calculated positions of well-covered part of human exome (according to Agilent SureSelect V5 Human All Exon, freely available here after registration).
Cosine_similarities_explained.R - simulations for explanation of signature threshold; stability analysis of similarity score between C. elegans and COAD/STAD signatures by random drawing from 95% confidence intervals and jack-knife bootstrapping.
homopolymer_analysis.R - analysis of homopolymers and 1-bp indels in homopolymers for C. elegans and human cancer samples.
nmSolve.R - contains function for non-negative matrix factorization.
Signatures_plots.R - calculation of adjustment coefficients between human exome and C. elegans genome, and plotting of respective contexts and adjusted signatures.
SNP_signature_analysis.R - analysis of COAD/STAD signature 8 and the ratio of synonimous to non-synonimous changes in the samples with a prevalence of this signature.
Signatures.xlsx - table with C. elegans mutation patterns, original and exome-adjusted, with and without 1-bp indel fractions; COAD/STAD signatures, with and without 1-bp indel fractions.
Session info with package versions for running the scripts:
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 bayesm_3.1-0.1 MASS_7.3-49 pROC_1.11.0
[5] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2 rtracklayer_1.36.6 gam_1.15
[9] foreach_1.4.4 dplyr_0.7.4 deconstructSigs_1.8.0 VariantAnnotation_1.22.3
[13] Rsamtools_1.28.0 Biostrings_2.44.2 XVector_0.16.0 SummarizedExperiment_1.6.5
[17] DelayedArray_0.3.0 matrixStats_0.53.1 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3
[21] IRanges_2.10.5 S4Vectors_0.14.7 reshape2_1.4.3 ggplot2_2.2.1
[25] mg14_0.0.5 devtools_1.13.5 NMF_0.21.0 Biobase_2.36.2
[29] BiocGenerics_0.22.1 cluster_2.0.6 rngtools_1.2.4 pkgmaker_0.22
[33] registry_0.5 tsne_0.1-3
loaded via a namespace (and not attached):
[1] bit64_0.9-7 assertthat_0.2.0 blob_1.1.1 GenomeInfoDbData_0.99.0 yaml_2.1.18 pillar_1.2.1 RSQLite_2.0 lattice_0.20-35
[9] glue_1.2.0 digest_0.6.15 RColorBrewer_1.1-2 colorspace_1.3-2 Matrix_1.2-12 plyr_1.8.4 XML_3.98-1.10 pkgconfig_2.0.1
[17] biomaRt_2.32.1 zlibbioc_1.22.0 xtable_1.8-2 scales_0.5.0 BiocParallel_1.10.1 tibble_1.4.2 withr_2.1.2 GenomicFeatures_1.28.5
[25] lazyeval_0.2.1 magrittr_1.5 memoise_1.1.0 doParallel_1.0.11 tools_3.4.4 gridBase_0.4-7 stringr_1.3.0 munsell_0.4.3
[33] AnnotationDbi_1.38.2 bindrcpp_0.2 compiler_3.4.4 rlang_0.2.0 grid_3.4.4 RCurl_1.95-4.10 iterators_1.0.9 bitops_1.0-6
[41] gtable_0.2.0 codetools_0.2-15 DBI_0.8 R6_2.2.2 GenomicAlignments_1.12.2 knitr_1.20 bit_1.1-12 bindr_0.1.1
[49] stringi_1.1.7 Rcpp_0.12.16
In case of any questions or enquiries, please contact Nadezda Volkova (nvolkova@ebi.ac.uk).
N. Volkova, B. Meier, M. Gerstung. EMBL-EBI, 2017.