{
  "_id": "6ac4f8b0f511ae58c09a3a3a",
  "Package": "SelectSim",
  "Title": "Selected Events Linked by Evolutionary Conditions in Cancer",
  "Version": "0.1.6",
  "Authors@R": "c(\nperson(\"Arvind\", \"Iyer\", , \"ayalurarvind@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-8247-700X\")),\nperson(\"Marco\", \"Mina\", , \"marco.mina.85@gmail.com\", role = \"aut\"),\nperson(\"Miljan\", \"Petrovic\", , \"miljanpet93@gmail.com\", role = c(\"aut\", \"cph\")),\nperson(\"Giovanni\", \"Ciriello\", , \"giovanni.ciriello@unil.ch\", role = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-2021-8683\"))\n)",
  "Description": "Implements the 'SelectSim' methodology for identifying\npatterns of co-occurrence and mutual exclusivity between\nfunctional genomic alterations in cancer cohorts. The package\nprocesses mutation annotation data, constructs alteration\nmatrices, estimates expected alteration-pair frequencies, and\nquantifies deviations associated with selective interactions.\nThe methodology is described in Iyer et al. (2026)\n<doi:10.1038/s41588-026-02661-4>.",
  "License": "MIT + file LICENSE",
  "URL": "https://csogroup.github.io/SelectSim/",
  "BugReports": "https://github.com/CSOgroup/SelectSim/issues",
  "VignetteBuilder": "knitr",
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  "Language": "en-US",
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  "Packaged": {
    "Date": "2026-10-06 13:27:27 UTC",
    "User": "root"
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  "Author": "Arvind Iyer [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-8247-700X>), Marco Mina [aut],\nMiljan Petrovic [aut, cph], Giovanni Ciriello [aut, cph]\n(ORCID: <https://orcid.org/0000-0003-2021-8683>)",
  "Maintainer": "Arvind Iyer <ayalurarvind@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-07-21 10:40:14 UTC",
  "RemoteUrl": "https://github.com/cran/SelectSim",
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  "_expires": "2027-01-14T13:33:33.000Z",
  "_created": "2026-10-06T13:27:27.000Z",
  "_published": "2026-10-06T13:33:36.503Z",
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    "description": "Computational biologist | Postdoctoral Researcher at UHN | A fast learner and a labeled nerd.",
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  "_exports": [
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    "al.pairwise.alteration.stats",
    "al.stats",
    "am.pairwise.alteration.coverage",
    "am.pairwise.alteration.overlap",
    "am.stats",
    "am.weight.pairwise.alteration.overlap",
    "binary.yule",
    "effectSize",
    "estimate_p_val",
    "estimate_pairwise_p",
    "estimateFDR2",
    "filter_maf_column",
    "filter_maf_complex",
    "filter_maf_gene.name",
    "filter_maf_ignore",
    "filter_maf_missense",
    "filter_maf_mutation.type",
    "filter_maf_mutations",
    "filter_maf_sample",
    "filter_maf_schema",
    "filter_maf_truncating",
    "generateS",
    "generateW_block",
    "generateW_mean_tmb",
    "GENIE_maf_schema",
    "get.blocks",
    "interaction.table",
    "maf2gam",
    "mutation_type",
    "new.AL.general",
    "new.ALS",
    "new.AMS",
    "null_model_parallel",
    "obs_exp_scatter",
    "overlap_pair_extract",
    "r.am.pairwise.alteration.overlap",
    "r.effectSize",
    "retrieveOutliers",
    "ridge_plot_ed",
    "ridge_plot_ed_compare",
    "selectX",
    "stat_maf_column",
    "stat_maf_gene",
    "stat_maf_sample",
    "TCGA_maf_schema",
    "template.obj.gen",
    "theme_Publication",
    "w.r.am.pairwise.alteration.overlap"
  ],
  "_datasets": [
    {
      "name": "luad_maf",
      "title": "Lung adenocarcinoma MAF from TCGA cohort",
      "object": "luad_maf",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chromosome",
        "Start_Position",
        "End_Position",
        "Hugo_Symbol",
        "Variant_Classification",
        "Tumor_Sample_Barcode",
        "sample",
        "HGVSp_Short"
      ],
      "rows": 220734,
      "table": true,
      "tojson": true
    },
    {
      "name": "luad_result",
      "title": "Lung adenocarcinoma from TCGA cohort as SelectSim run results",
      "object": "luad_result",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SFE_1",
        "SFE_2",
        "name",
        "support_1",
        "support_2",
        "freq_1",
        "freq_2",
        "overlap",
        "w_overlap",
        "max_overlap",
        "freq_overlap",
        "r_overlap",
        "w_r_overlap",
        "wES",
        "wFDR",
        "nES",
        "mean_r_nES",
        "nFDR",
        "cum_freq",
        "nFDR2",
        "type",
        "FDR"
      ],
      "rows": 253,
      "table": true,
      "tojson": true
    },
    {
      "name": "luad_run_data",
      "title": "Lung adenocarcinoma from TCGA cohort as SelectSim run object",
      "object": "luad_run_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "oncokb_genes",
      "title": "OncoKB v3.9 cancer genes",
      "object": "oncokb_genes",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "oncokb_truncating_genes",
      "title": "OncoKB v3.9 cancer genes consider for truncating mutations",
      "object": "oncokb_truncating_genes",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "variant_catalogue",
      "title": "OncoKB v3.9 cancer genes",
      "object": "variant_catalogue",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "mut",
        "oncogenic"
      ],
      "rows": 2478,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add",
      "title": "Sum a list of matrices element-wise",
      "topics": [
        "add"
      ]
    },
    {
      "page": "al.pairwise.alteration.stats",
      "title": "Compute pairwise alteration statistics for an alteration landscape",
      "topics": [
        "al.pairwise.alteration.stats"
      ]
    },
    {
      "page": "al.stats",
      "title": "Compute alteration landscape statistics",
      "topics": [
        "al.stats"
      ]
    },
    {
      "page": "am.pairwise.alteration.coverage",
      "title": "Compute pairwise alteration coverage statistics",
      "topics": [
        "am.pairwise.alteration.coverage"
      ]
    },
    {
      "page": "am.pairwise.alteration.overlap",
      "title": "Compute pairwise alteration co-occurrence counts",
      "topics": [
        "am.pairwise.alteration.overlap"
      ]
    },
    {
      "page": "am.stats",
      "title": "Compute summary statistics for a binary alteration matrix",
      "topics": [
        "am.stats"
      ]
    },
    {
      "page": "am.weight.pairwise.alteration.overlap",
      "title": "Compute TMB-weighted pairwise alteration overlap",
      "topics": [
        "am.weight.pairwise.alteration.overlap"
      ]
    },
    {
      "page": "binary.yule",
      "title": "Compute Yule Q coefficient for all gene pairs",
      "topics": [
        "binary.yule"
      ]
    },
    {
      "page": "effectSize",
      "title": "Compute effect size between observed and expected overlap",
      "topics": [
        "effectSize"
      ]
    },
    {
      "page": "estimate_p_val",
      "title": "Compute empirical two-sided p-value for a gene pair",
      "topics": [
        "estimate_p_val"
      ]
    },
    {
      "page": "estimate_pairwise_p",
      "title": "Compute p-values for all gene pairs in a results table",
      "topics": [
        "estimate_pairwise_p"
      ]
    },
    {
      "page": "estimateFDR2",
      "title": "Estimate FDR by scanning observed vs null effect sizes",
      "topics": [
        "estimateFDR2"
      ]
    },
    {
      "page": "filter_maf_column",
      "title": "Filter maf function",
      "topics": [
        "filter_maf_column"
      ]
    },
    {
      "page": "filter_maf_complex",
      "title": "Filter a MAF dataframe by a combination of column values",
      "topics": [
        "filter_maf_complex"
      ]
    },
    {
      "page": "filter_maf_gene.name",
      "title": "Filter a MAF dataframe by gene name",
      "topics": [
        "filter_maf_gene.name"
      ]
    },
    {
      "page": "filter_maf_ignore",
      "title": "This function filters a MAF dataframe by retaining (or discarding) ignore mutations",
      "topics": [
        "filter_maf_ignore"
      ]
    },
    {
      "page": "filter_maf_missense",
      "title": "This function filters a MAF dataframe by retaining (or discarding) missense mutations",
      "topics": [
        "filter_maf_missense"
      ]
    },
    {
      "page": "filter_maf_mutation.type",
      "title": "Filter a MAF dataframe by mutation type",
      "topics": [
        "filter_maf_mutation.type"
      ]
    },
    {
      "page": "filter_maf_mutations",
      "title": "Filter a MAF dataframe by specific gene-mutation combinations",
      "topics": [
        "filter_maf_mutations"
      ]
    },
    {
      "page": "filter_maf_sample",
      "title": "Filter a MAF dataframe by sample ID",
      "topics": [
        "filter_maf_sample"
      ]
    },
    {
      "page": "filter_maf_schema",
      "title": "This function filters a MAF dataframe by sample id",
      "topics": [
        "filter_maf_schema"
      ]
    },
    {
      "page": "filter_maf_truncating",
      "title": "This function filters a MAF dataframe by retaining (or discarding) truncating mutations",
      "topics": [
        "filter_maf_truncating"
      ]
    },
    {
      "page": "generateS",
      "title": "Generate S matrix",
      "topics": [
        "generateS"
      ]
    },
    {
      "page": "generateW_block",
      "title": "Generate block-aware sample weight matrix",
      "topics": [
        "generateW_block"
      ]
    },
    {
      "page": "generateW_mean_tmb",
      "title": "Generate sample weight matrix from TMB values",
      "topics": [
        "generateW_mean_tmb"
      ]
    },
    {
      "page": "GENIE_maf_schema",
      "title": "GENIE_maf_schema: schema for GENIE maf file to process the mutations",
      "topics": [
        "GENIE_maf_schema"
      ]
    },
    {
      "page": "get.blocks",
      "title": "Get sample/alteration blocks",
      "topics": [
        "get.blocks"
      ]
    },
    {
      "page": "interaction.table",
      "title": "Build the full interaction results table from selectX outputs",
      "topics": [
        "interaction.table"
      ]
    },
    {
      "page": "luad_maf",
      "title": "Lung adenocarcinoma MAF from TCGA cohort",
      "topics": [
        "luad_maf"
      ]
    },
    {
      "page": "luad_result",
      "title": "Lung adenocarcinoma from TCGA cohort as SelectSim run results",
      "topics": [
        "luad_result"
      ]
    },
    {
      "page": "luad_run_data",
      "title": "Lung adenocarcinoma from TCGA cohort as SelectSim run object",
      "topics": [
        "luad_run_data"
      ]
    },
    {
      "page": "maf2gam",
      "title": "Generate gam from the maf file",
      "topics": [
        "maf2gam"
      ]
    },
    {
      "page": "mutation_type",
      "title": "Mutation list object",
      "topics": [
        "mutation_type"
      ]
    },
    {
      "page": "new.AL.general",
      "title": "Create an Alteration Landscape (AL) object",
      "topics": [
        "new.AL.general"
      ]
    },
    {
      "page": "new.ALS",
      "title": "Initialize an Alteration Landscape Stats (ALS) container",
      "topics": [
        "new.ALS"
      ]
    },
    {
      "page": "new.AMS",
      "title": "Initialize an Alteration Matrix Stats (AMS) container",
      "topics": [
        "new.AMS"
      ]
    },
    {
      "page": "null_model_parallel",
      "title": "Generating the null_simulation matrix",
      "topics": [
        "null_model_parallel"
      ]
    },
    {
      "page": "obs_exp_scatter",
      "title": "Scatter plot of observed vs expected weighted co-mutation",
      "topics": [
        "obs_exp_scatter"
      ]
    },
    {
      "page": "oncokb_genes",
      "title": "OncoKB v3.9 cancer genes",
      "topics": [
        "oncokb_genes"
      ]
    },
    {
      "page": "oncokb_truncating_genes",
      "title": "OncoKB v3.9 cancer genes consider for truncating mutations",
      "topics": [
        "oncokb_truncating_genes"
      ]
    },
    {
      "page": "overlap_pair_extract",
      "title": "Extract null-model weighted overlap distribution for a gene pair",
      "topics": [
        "overlap_pair_extract"
      ]
    },
    {
      "page": "r.am.pairwise.alteration.overlap",
      "title": "Compute null overlap matrix",
      "topics": [
        "r.am.pairwise.alteration.overlap"
      ]
    },
    {
      "page": "r.effectSize",
      "title": "Compute effect sizes for null model permutations",
      "topics": [
        "r.effectSize"
      ]
    },
    {
      "page": "retrieveOutliers",
      "title": "Identify outlier null-model matrices",
      "topics": [
        "retrieveOutliers"
      ]
    },
    {
      "page": "ridge_plot_ed",
      "title": "Ridge plot of null-model background distribution for significant gene pairs",
      "topics": [
        "ridge_plot_ed"
      ]
    },
    {
      "page": "ridge_plot_ed_compare",
      "title": "Ridge plot comparing null-model distributions for two datasets",
      "topics": [
        "ridge_plot_ed_compare"
      ]
    },
    {
      "page": "selectX",
      "title": "SelectX main function from SelectSim to create alteration object with background model",
      "topics": [
        "selectX"
      ]
    },
    {
      "page": "stat_maf_column",
      "title": "Summary functions for MAF file",
      "topics": [
        "stat_maf_column"
      ]
    },
    {
      "page": "stat_maf_gene",
      "title": "Count mutations per gene in a MAF file",
      "topics": [
        "stat_maf_gene"
      ]
    },
    {
      "page": "stat_maf_sample",
      "title": "Count mutations per sample in a MAF file",
      "topics": [
        "stat_maf_sample"
      ]
    },
    {
      "page": "TCGA_maf_schema",
      "title": "TCGA_maf_schema: schema for TCGA maf file to process the mutations",
      "topics": [
        "TCGA_maf_schema"
      ]
    },
    {
      "page": "template.obj.gen",
      "title": "Generate the template matrix",
      "topics": [
        "template.obj.gen"
      ]
    },
    {
      "page": "theme_Publication",
      "title": "A clean ggplot2 theme for publication-quality plots",
      "topics": [
        "theme_Publication"
      ]
    },
    {
      "page": "variant_catalogue",
      "title": "OncoKB v3.9 cancer genes",
      "topics": [
        "variant_catalogue"
      ]
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