GENIE_maf_schema        GENIE_maf_schema: schema for GENIE maf file to
                        process the mutations
TCGA_maf_schema         TCGA_maf_schema: schema for TCGA maf file to
                        process the mutations
add                     Sum a list of matrices element-wise
al.pairwise.alteration.stats
                        Compute pairwise alteration statistics for an
                        alteration landscape
al.stats                Compute alteration landscape statistics
am.pairwise.alteration.coverage
                        Compute pairwise alteration coverage statistics
am.pairwise.alteration.overlap
                        Compute pairwise alteration co-occurrence
                        counts
am.stats                Compute summary statistics for a binary
                        alteration matrix
am.weight.pairwise.alteration.overlap
                        Compute TMB-weighted pairwise alteration
                        overlap
binary.yule             Compute Yule Q coefficient for all gene pairs
effectSize              Compute effect size between observed and
                        expected overlap
estimateFDR2            Estimate FDR by scanning observed vs null
                        effect sizes
estimate_p_val          Compute empirical two-sided p-value for a gene
                        pair
estimate_pairwise_p     Compute p-values for all gene pairs in a
                        results table
filter_maf_column       Filter maf function
filter_maf_complex      Filter a MAF dataframe by a combination of
                        column values
filter_maf_gene.name    Filter a MAF dataframe by gene name
filter_maf_ignore       This function filters a MAF dataframe by
                        retaining (or discarding) ignore mutations
filter_maf_missense     This function filters a MAF dataframe by
                        retaining (or discarding) missense mutations
filter_maf_mutation.type
                        Filter a MAF dataframe by mutation type
filter_maf_mutations    Filter a MAF dataframe by specific
                        gene-mutation combinations
filter_maf_sample       Filter a MAF dataframe by sample ID
filter_maf_schema       This function filters a MAF dataframe by sample
                        id
filter_maf_truncating   This function filters a MAF dataframe by
                        retaining (or discarding) truncating mutations
generateS               Generate S matrix
generateW_block         Generate block-aware sample weight matrix
generateW_mean_tmb      Generate sample weight matrix from TMB values
get.blocks              Get sample/alteration blocks
interaction.table       Build the full interaction results table from
                        selectX outputs
luad_maf                Lung adenocarcinoma MAF from TCGA cohort
luad_result             Lung adenocarcinoma from TCGA cohort as
                        SelectSim run results
luad_run_data           Lung adenocarcinoma from TCGA cohort as
                        SelectSim run object
maf2gam                 Generate gam from the maf file
mutation_type           Mutation list object
new.AL.general          Create an Alteration Landscape (AL) object
new.ALS                 Initialize an Alteration Landscape Stats (ALS)
                        container
new.AMS                 Initialize an Alteration Matrix Stats (AMS)
                        container
null_model_parallel     Generating the null_simulation matrix
obs_exp_scatter         Scatter plot of observed vs expected weighted
                        co-mutation
oncokb_genes            OncoKB v3.9 cancer genes
oncokb_truncating_genes
                        OncoKB v3.9 cancer genes consider for
                        truncating mutations
overlap_pair_extract    Extract null-model weighted overlap
                        distribution for a gene pair
r.am.pairwise.alteration.overlap
                        Compute null overlap matrix
r.effectSize            Compute effect sizes for null model
                        permutations
retrieveOutliers        Identify outlier null-model matrices
ridge_plot_ed           Ridge plot of null-model background
                        distribution for significant gene pairs
ridge_plot_ed_compare   Ridge plot comparing null-model distributions
                        for two datasets
selectX                 SelectX main function from SelectSim to create
                        alteration object with background model
stat_maf_column         Summary functions for MAF file
stat_maf_gene           Count mutations per gene in a MAF file
stat_maf_sample         Count mutations per sample in a MAF file
template.obj.gen        Generate the template matrix
theme_Publication       A clean ggplot2 theme for publication-quality
                        plots
variant_catalogue       OncoKB v3.9 cancer genes
w.r.am.pairwise.alteration.overlap
                        Compute null weighted overlap matrix
