Function reference
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GENIE_maf_schema - GENIE_maf_schema: GENIE_maf_schema: schema for TCGA maf file to process the mutations
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TCGA_maf_schema - TCGA_maf_schema: schema for TCGA maf file to process the mutations
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add() - Compute weight overlap stats
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al.pairwise.alteration.stats() - Compute weight overlap stats
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al.stats() - Create an alteration stats object
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am.pairwise.alteration.coverage() - Compute weight overlap stats
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am.pairwise.alteration.overlap() - Compute overlap stats
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am.stats() - Create an alteration matrix stats object
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am.weight.pairwise.alteration.overlap() - Compute weight overlap stats
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binary.yule() - Compute yule coefficent
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effectSize() - Compute weight overlap stats
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estimateFDR2() - Compute FDR
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estimate_p_val() - Compute pairwise p-value
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estimate_pairwise_p() - Compute pairwise p-value
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filter_maf_column() - Filter maf function
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filter_maf_complex() - This function filters a MAF dataframe by retaining only the rows with a combination of values compatible with the values
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filter_maf_gene.name() - This function filters a MAF dataframe by sample id
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filter_maf_ignore() - This function filters a MAF dataframe by retaining (or discarding) ignore mutations
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filter_maf_missense() - This function filters a MAF dataframe by retaining (or discarding) missense mutations
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filter_maf_mutation.type() - This function filters a MAF dataframe by sample id
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filter_maf_mutations() - This function filters a MAF dataframe by sample id
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filter_maf_sample() - This function filters a MAF dataframe by sample id
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filter_maf_schema() - This function filters a MAF dataframe by sample id
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filter_maf_truncating() - This function filters a MAF dataframe by retaining (or discarding) truncating mutations
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generateS() - Generate S matrix
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generateW_block() - Generating the weight matrix taking sample covariate
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generateW_mean_tmb() - Generating the weight matrix
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get.blocks() - Get sample/alteration blocks
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interaction.table() - Compute weight overlap stats
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luad_maf - Lung adenocarcinoma MAF from TCGA cohort
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luad_result - Lung adenocarcinoma from TCGA cohort as selectX run results
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luad_run_data - Lung adenocarcinoma from TCGA cohort as selectX run object
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maf2gam() - Generate gam from the maf file
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mutation_type - Mutation list object
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new.AL.general() - Create an AL object
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new.ALS() - Create an alteration landscape object
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new.AMS() - Create an alteration matrix stats object
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null_model_parallel() - Generating the null_simulation matrix
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null_model_parallel_debug() - Generating the null_simulation matrix
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obs_exp_scatter() - Create an AL object
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oncokb_genes - OncoKB v3.9 cancer genes
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oncokb_truncating_genes - OncoKB v3.9 cancer genes consider for truncating mutations
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overlap_pair_extract() - Extract the backgroun distribution
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r.am.pairwise.alteration.overlap() - Compute weight overlap stats
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r.effectSize() - Compute weight overlap stats
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retrieveOutliers() - Removing the Outliers
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ridge_plot_ed() - Generate a pairs background plot
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ridge_plot_ed_compare() - Generate a pairs background plot for two dataset comaprision
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selectX() - SelectX main function to create alteration object with background model
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selectX_debug() - SelectX main function to create alteration object with background model
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stat_maf_column() - Summary functions for MAF file
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stat_maf_gene() - Summary functions for MAF file
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stat_maf_sample() - Summary functions for MAF file
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templeate.obj.gen() - Generating the template matrix
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variant_catalogue - OncoKB v3.9 cancer genes
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w.r.am.pairwise.alteration.overlap() - Compute weight overlap stats