add	add
al.pairwise.alteration.stats	al.pairwise.alteration.stats
al.stats	al.stats
am.pairwise.alteration.coverage	am.pairwise.alteration.coverage
am.pairwise.alteration.overlap	am.pairwise.alteration.overlap
am.stats	am.stats
am.weight.pairwise.alteration.overlap	am.weight.pairwise.alteration.overlap
binary.yule	binary.yule
effectSize	effectSize
estimateFDR2	estimateFDR2
estimate_pairwise_p	estimate_pairwise_p
estimate_p_val	estimate_p_val
filter_maf_column	filter_maf_column
filter_maf_complex	filter_maf_complex
filter_maf_gene.name	filter_maf_gene.name
filter_maf_ignore	filter_maf_ignore
filter_maf_missense	filter_maf_missense
filter_maf_mutation.type	filter_maf_mutation.type
filter_maf_mutations	filter_maf_mutations
filter_maf_sample	filter_maf_sample
filter_maf_schema	filter_maf_schema
filter_maf_truncating	filter_maf_truncating
generateS	generateS
generateW_block	generateW_block
generateW_mean_tmb	generateW_mean_tmb
GENIE_maf_schema	GENIE_maf_schema
get.blocks	get.blocks
interaction.table	interaction.table
luad_maf	luad_maf
luad_result	luad_result
luad_run_data	luad_run_data
maf2gam	maf2gam
mutation_type	mutation_type
new.AL.general	new.AL.general
new.ALS	new.ALS
new.AMS	new.AMS
null_model_parallel	null_model_parallel
obs_exp_scatter	obs_exp_scatter
oncokb_genes	oncokb_genes
oncokb_truncating_genes	oncokb_truncating_genes
overlap_pair_extract	overlap_pair_extract
r.am.pairwise.alteration.overlap	r.am.pairwise.alteration.overlap
r.effectSize	r.effectSize
retrieveOutliers	retrieveOutliers
ridge_plot_ed	ridge_plot_ed
ridge_plot_ed_compare	ridge_plot_ed_compare
selectX	selectX
stat_maf_column	stat_maf_column
stat_maf_gene	stat_maf_gene
stat_maf_sample	stat_maf_sample
TCGA_maf_schema	TCGA_maf_schema
template.obj.gen	template.obj.gen
theme_Publication	theme_Publication
variant_catalogue	variant_catalogue
w.r.am.pairwise.alteration.overlap	w.r.am.pairwise.alteration.overlap
