# Selected Events Linked by Evolutionary Conditions in Cancer

## Documentation for package ‘SelectSim’ version 0.1.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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_pairwise_p | Compute p-values for all gene pairs in a results table
estimate_p_val | Compute empirical two-sided p-value for a gene pair
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
GENIE_maf_schema | GENIE_maf_schema: schema for GENIE maf file to process the mutations
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
TCGA_maf_schema | TCGA_maf_schema: schema for TCGA maf file to process the mutations
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