Package: SelectSim 0.1.6

Arvind Iyer

SelectSim: Selected Events Linked by Evolutionary Conditions in Cancer

Implements the 'SelectSim' methodology for identifying patterns of co-occurrence and mutual exclusivity between functional genomic alterations in cancer cohorts. The package processes mutation annotation data, constructs alteration matrices, estimates expected alteration-pair frequencies, and quantifies deviations associated with selective interactions. The methodology is described in Iyer et al. (2026) <doi:10.1038/s41588-026-02661-4>.

Authors:Arvind Iyer [aut, cre, cph], Marco Mina [aut], Miljan Petrovic [aut, cph], Giovanni Ciriello [aut, cph]

SelectSim_0.1.6.tar.gz
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SelectSim_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SelectSim/json (API)

# Install 'SelectSim' in R:
install.packages('SelectSim', repos = c('https://csogroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/csogroup/selectsim/issues

Pkgdown/docs site:https://csogroup.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

openblascpp

4.78 score 3 stars 49 exports 87 dependencies

Last updated from:54c06ec5f7. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK192
linux-devel-x86_64OK233
source / vignettesOK258
linux-release-arm64OK180
linux-release-x86_64OK278
macos-release-arm64OK260
macos-release-x86_64OK337
macos-oldrel-arm64OK222
macos-oldrel-x86_64OK446
windows-develOK186
windows-releaseOK179
windows-oldrelOK183
wasm-releaseOK158

Exports:addal.pairwise.alteration.statsal.statsam.pairwise.alteration.coverageam.pairwise.alteration.overlapam.statsam.weight.pairwise.alteration.overlapbinary.yuleeffectSizeestimate_p_valestimate_pairwise_pestimateFDR2filter_maf_columnfilter_maf_complexfilter_maf_gene.namefilter_maf_ignorefilter_maf_missensefilter_maf_mutation.typefilter_maf_mutationsfilter_maf_samplefilter_maf_schemafilter_maf_truncatinggenerateSgenerateW_blockgenerateW_mean_tmbGENIE_maf_schemaget.blocksinteraction.tablemaf2gammutation_typenew.AL.generalnew.ALSnew.AMSnull_model_parallelobs_exp_scatteroverlap_pair_extractr.am.pairwise.alteration.overlapr.effectSizeretrieveOutliersridge_plot_edridge_plot_ed_compareselectXstat_maf_columnstat_maf_genestat_maf_sampleTCGA_maf_schematemplate.obj.gentheme_Publicationw.r.am.pairwise.alteration.overlap

Dependencies:abindbackportsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11DerivdigestdoBydoParalleldoRNGdplyrfarverforeachforecastFormulafracdiffgenericsggplot2ggpubrggrepelggridgesggsciggsignifgluegridExtragtableisobanditeratorslabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvminqamodelrnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasRfastrlangrngtoolsrstatixS7scalesSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrziggzoo

Data Processing with SelectSim
Installation | Example | Generating the GAMs | Generating the run_object to run SelectSim | Session information
Rendered fromdata_processing.Rmdusingknitr::rmarkdown

Last update: 2026-07-12
Started: 2024-08-23

Introduction to SelectSim
Installation | Example | Data Description & Format | Running SelectSim | Interpreting the results | Filtering significant hits | Plotting a scatter plot of co-mutation | Session information
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-07-12
Started: 2024-08-23

Readme and manuals

Help Manual

Help pageTopics
Sum a list of matrices element-wiseadd
Compute pairwise alteration statistics for an alteration landscapeal.pairwise.alteration.stats
Compute alteration landscape statisticsal.stats
Compute pairwise alteration coverage statisticsam.pairwise.alteration.coverage
Compute pairwise alteration co-occurrence countsam.pairwise.alteration.overlap
Compute summary statistics for a binary alteration matrixam.stats
Compute TMB-weighted pairwise alteration overlapam.weight.pairwise.alteration.overlap
Compute Yule Q coefficient for all gene pairsbinary.yule
Compute effect size between observed and expected overlapeffectSize
Compute empirical two-sided p-value for a gene pairestimate_p_val
Compute p-values for all gene pairs in a results tableestimate_pairwise_p
Estimate FDR by scanning observed vs null effect sizesestimateFDR2
Filter maf functionfilter_maf_column
Filter a MAF dataframe by a combination of column valuesfilter_maf_complex
Filter a MAF dataframe by gene namefilter_maf_gene.name
This function filters a MAF dataframe by retaining (or discarding) ignore mutationsfilter_maf_ignore
This function filters a MAF dataframe by retaining (or discarding) missense mutationsfilter_maf_missense
Filter a MAF dataframe by mutation typefilter_maf_mutation.type
Filter a MAF dataframe by specific gene-mutation combinationsfilter_maf_mutations
Filter a MAF dataframe by sample IDfilter_maf_sample
This function filters a MAF dataframe by sample idfilter_maf_schema
This function filters a MAF dataframe by retaining (or discarding) truncating mutationsfilter_maf_truncating
Generate S matrixgenerateS
Generate block-aware sample weight matrixgenerateW_block
Generate sample weight matrix from TMB valuesgenerateW_mean_tmb
GENIE_maf_schema: schema for GENIE maf file to process the mutationsGENIE_maf_schema
Get sample/alteration blocksget.blocks
Build the full interaction results table from selectX outputsinteraction.table
Lung adenocarcinoma MAF from TCGA cohortluad_maf
Lung adenocarcinoma from TCGA cohort as SelectSim run resultsluad_result
Lung adenocarcinoma from TCGA cohort as SelectSim run objectluad_run_data
Generate gam from the maf filemaf2gam
Mutation list objectmutation_type
Create an Alteration Landscape (AL) objectnew.AL.general
Initialize an Alteration Landscape Stats (ALS) containernew.ALS
Initialize an Alteration Matrix Stats (AMS) containernew.AMS
Generating the null_simulation matrixnull_model_parallel
Scatter plot of observed vs expected weighted co-mutationobs_exp_scatter
OncoKB v3.9 cancer genesoncokb_genes
OncoKB v3.9 cancer genes consider for truncating mutationsoncokb_truncating_genes
Extract null-model weighted overlap distribution for a gene pairoverlap_pair_extract
Compute null overlap matrixr.am.pairwise.alteration.overlap
Compute effect sizes for null model permutationsr.effectSize
Identify outlier null-model matricesretrieveOutliers
Ridge plot of null-model background distribution for significant gene pairsridge_plot_ed
Ridge plot comparing null-model distributions for two datasetsridge_plot_ed_compare
SelectX main function from SelectSim to create alteration object with background modelselectX
Summary functions for MAF filestat_maf_column
Count mutations per gene in a MAF filestat_maf_gene
Count mutations per sample in a MAF filestat_maf_sample
TCGA_maf_schema: schema for TCGA maf file to process the mutationsTCGA_maf_schema
Generate the template matrixtemplate.obj.gen
A clean ggplot2 theme for publication-quality plotstheme_Publication
OncoKB v3.9 cancer genesvariant_catalogue
Compute null weighted overlap matrixw.r.am.pairwise.alteration.overlap