YAPSA-package	YAPSA
add_annotation	add_annotation
add_as_fist_to_list	add_as_fist_to_list
aggregate_exposures_by_category	aggregate_exposures_by_category
AlexCosmicArtif_sigInd_df	sigs
AlexCosmicArtif_sig_df	sigs
AlexCosmicValid_sigInd_df	sigs
AlexCosmicValid_sig_df	sigs
AlexInitialArtif_sigInd_df	sigs
AlexInitialArtif_sig_df	sigs
AlexInitialValid_sigInd_df	sigs
AlexInitialValid_sig_df	sigs
annotate_intermut_dist_cohort	annotate_intermut_dist_cohort
annotate_intermut_dist_PID	annotate_intermut_dist_PID
annotation_exposures_barplot	annotation_exposures_barplot
annotation_heatmap_exposures	annotation_heatmap_exposures
attribute_nucleotide_exchanges	attribute_nucleotide_exchanges
average_over_present	normalize_df_per_dim
build_gene_list_for_pathway	build_gene_list_for_pathway
chosen_AlexInitialArtif_sigInd_df	exampleYAPSA
chosen_signatures_indices_df	exampleYAPSA
compare_exposures	compare_exposures
compare_sets	compare_sets
compare_SMCs	compare_SMCs
compare_to_catalogues	compare_to_catalogues
complex_heatmap_exposures	complex_heatmap_exposures
compute_comparison_stat_df	compute_comparison_stat_df
cosineDist	cosineDist
COSMIC_subgroups_df	exampleYAPSA
create_mutation_catalogue_from_df	create_mutation_catalogue_from_df
create_mutation_catalogue_from_VR	create_mutation_catalogue_from_VR
cutoffCosmicArtif_abs_df	cutoffs
cutoffCosmicArtif_rel_df	cutoffs
cutoffCosmicValid_abs_df	cutoffs
cutoffCosmicValid_rel_df	cutoffs
cutoffInitialArtif_abs_df	cutoffs
cutoffInitialArtif_rel_df	cutoffs
cutoffInitialValid_abs_df	cutoffs
cutoffInitialValid_rel_df	cutoffs
cutoffs	cutoffs
cut_breaks_as_intervals	cut_breaks_as_intervals
exampleYAPSA	exampleYAPSA
exchange_colour_vector	exchange_colour_vector
exposures_barplot	exposures_barplot
extract_names_from_gene_list	extract_names_from_gene_list
find_affected_PIDs	find_affected_PIDs
get_extreme_PIDs	get_extreme_PIDs
hclust_exposures	hclust_exposures
LCD	LCD
LCD_complex_cutoff	LCD_complex_cutoff
LCD_complex_cutoff_perPID	LCD_complex_cutoff
lymphoma_Nature2013_COSMIC_cutoff_exposures_df	exampleYAPSA
lymphoma_Nature2013_raw_df	exampleYAPSA
lymphoma_PID_df	exampleYAPSA
lymphoma_test_df	exampleYAPSA
makeVRangesFromDataFrame	makeVRangesFromDataFrame
make_catalogue_strata_df	make_catalogue_strata_df
make_comparison_matrix	make_comparison_matrix
make_strata_df	make_strata_df
make_subgroups_df	make_subgroups_df
melt_exposures	melt_exposures
merge_exposures	merge_exposures
normalizeMotifs_otherRownames	normalizeMotifs_otherRownames
normalize_df_per_dim	normalize_df_per_dim
plotExchangeSpectra	plotExchangeSpectra
plot_exposures	plot_exposures
plot_relative_exposures	plot_exposures
plot_SMC	plot_SMC
plot_strata	plot_strata
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df	exampleYAPSA
repeat_df	repeat_df
run_annotate_vcf_pl	run_annotate_vcf_pl
run_comparison_catalogues	run_comparison_catalogues
run_comparison_general	run_comparison_general
run_kmer_frequency_correction	run_kmer_frequency_correction
run_kmer_frequency_normalization	run_kmer_frequency_normalization
run_plot_strata_general	run_plot_strata_general
run_SMC	run_SMC
sd_over_present	normalize_df_per_dim
shapiro_if_possible	shapiro_if_possible
sigs	sigs
split_exposures_by_subgroups	split_exposures_by_subgroups
stat_plot_subgroups	stat_plot_subgroups
stat_test_SMC	stat_test_SMC
stat_test_subgroups	stat_test_subgroups
stderrmean	stderrmean
stderrmean_over_present	normalize_df_per_dim
sum_over_list_of_df	sum_over_list_of_df
targetCapture_cor_factors	targetCapture_cor_factors
test_exposureAffected	test_exposureAffected
test_gene_list_in_exposures	test_gene_list_in_exposures
transform_rownames_deconstructSigs_to_YAPSA	transform_rownames_R_to_MATLAB
transform_rownames_MATLAB_to_R	transform_rownames_R_to_MATLAB
transform_rownames_nature_to_R	transform_rownames_R_to_MATLAB
transform_rownames_R_to_MATLAB	transform_rownames_R_to_MATLAB
transform_rownames_YAPSA_to_deconstructSigs	transform_rownames_R_to_MATLAB
translate_to_1kG	translate_to_hg19
translate_to_hg19	translate_to_hg19
trellis_rainfall_plot	trellis_rainfall_plot
YAPSA	YAPSA
