CNAqc-package	CNAqc-package
%>%	pipe
analyze_peaks	analyze_peaks
annotate_variants	annotate_variants
as_maftools_cohort	as_maftools_cohort
as_maftools_obj	as_maftools_obj
augment_with_maf	augment_with_maf
augment_with_vep	augment_with_vep
auto_tolerance	auto_tolerance
CCF	CCF
chr_coordinates_GRCh38	chr_coordinates_GRCh38
chr_coordinates_GRCm38	chr_coordinates_GRCm38
chr_coordinates_hg19	chr_coordinates_hg19
CNA	CNA
CNAqc	CNAqc-package
CNA_gene	CNA_gene
compute_CCF	compute_CCF
detect_arm_overfragmentation	detect_arm_overfragmentation
example_dataset_CNAqc	example_dataset_CNAqc
example_PCAWG	example_PCAWG
fpr_test	fpr_test
gene_coordinates_GRCh38	gene_coordinates_GRCh38
gene_coordinates_hg19	gene_coordinates_hg19
get_drivers	get_drivers
get_mCNAqc_stats	get_mCNAqc_stats
get_PASS_percentage	get_PASS_percentage
get_sample	get_sample
get_sample_name	get_sample_name
init	init
inspect_segment	inspect_segment
intogen_drivers	intogen_drivers
multisample_init	multisample_init
Mutations	Mutations
parse_Battenberg	parse_Battenberg
plot.cnaqc	plot.cnaqc
plot.m_cnaqc	plot.m_cnaqc
plot_arm_fragmentation	plot_arm_fragmentation
plot_CCF	plot_CCF
plot_data_histogram	plot_data_histogram
plot_gw_ccf	plot_gw_ccf
plot_gw_counts	plot_gw_counts
plot_gw_depth	plot_gw_depth
plot_gw_vaf	plot_gw_vaf
plot_icon_CNA	plot_icon_CNA
plot_karyotypes	plot_karyotypes
plot_multisample_CNA	plot_multisample_CNA
plot_peaks_analysis	plot_peaks_analysis
plot_qc	plot_qc
plot_SBS	plot_SBS
plot_segments	plot_segments
plot_segments_multisample	plot_segments_multisample
plot_segment_size_distribution	plot_segment_size_distribution
plot_smoothing	plot_smoothing
print.cnaqc	print.cnaqc
print.m_cnaqc	print.m_cnaqc
SBS	SBS
SBS_counts	SBS_counts
smooth_segments	smooth_segments
split_by_chromosome	split_by_chromosome
subsample	subsample
subset_by_minimum_CCF	subset_by_minimum_CCF
subset_by_segment_karyotype	subset_by_segment_karyotype
subset_by_segment_minmutations	subset_by_segment_minmutations
subset_by_segment_totalcn	subset_by_segment_totalcn
subset_snvs	subset_snvs
wt_mutant_alleles	wt_mutant_alleles
