# CNAqc - Copy Number Analysis quality check

## Documentation for package ‘CNAqc’ version 1.1.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

analyze_peaks | QC by peak-detection algorithms.
annotate_variants | Annotate variants and drivers.
as_maftools_cohort | Convert a list of CNAqc object to a maftools object.
as_maftools_obj | Convert a CNAqc object to a maftools object.
augment_with_maf | Import MAF annotations.
augment_with_vep | Import VEP annotations.
auto_tolerance | Determine the optimal error tolerance to QC clonal simple CNAs.
CCF | Extract CCF estimates.
chr_coordinates_GRCh38 | Coordinates for GRCh38 chromosomes.
chr_coordinates_GRCm38 | Coordinates for GRCm38 chromosomes.
chr_coordinates_hg19 | Coordinates for hg19 chromosomes.
CNA | Extract CNAs.
CNA_gene | Extract per-gene copy number status.
compute_CCF | Compute CCF values.
detect_arm_overfragmentation | Determines arm-level over-fragmentation patterns.
example_dataset_CNAqc | Example CNAqc dataset.
example_PCAWG | Example PCAWG tumour
fpr_test | Data (simulation performance) from the trainig set to auto-tune epsilon.
gene_coordinates_GRCh38 | Coordinates for GRCh38 genes
gene_coordinates_hg19 | Coordinates for hg19 genes
get_drivers | Extract drivers data.
get_mCNAqc_stats | Get mCNAqc statistics
get_PASS_percentage | Returns percentage of passed segments
get_sample | get desidered samples
get_sample_name | get sample names from CNAqc and mCNAqc objects
init | Creates a CNAqc object.
inspect_segment | Plot VAFs across chromosomes.
intogen_drivers | List of Intogen driver genes per tumour type.
multisample_init | Create multisample segmentation
Mutations | Extract mutations.
parse_Battenberg | Parse Battenberg calls.
plot.cnaqc | Plot for class "cnaqc".
plot.m_cnaqc | Plot for class "m_cnaqc".
plot_arm_fragmentation | Plot the arm level fragmentation test.
plot_CCF | Plot the CCF estimates in the data.
plot_data_histogram | Plot the read-counts data histograms.
plot_gw_ccf | Plot genome-wide CCFs.
plot_gw_counts | Plot genome-wide mutation counts.
plot_gw_depth | Plot genome-wide coverage.
plot_gw_vaf | Plot genome-wide VAFs.
plot_icon_CNA | A circular plot for simple clonal CNAs.
plot_karyotypes | Plot counts and numbers of clonal simple CNAs.
plot_multisample_CNA | Plots CNAs from multiple samples.
plot_peaks_analysis | Plot the results of peak analysis.
plot_qc | Plot a summary of QC results.
plot_SBS | Plost SBS counts
plot_segments | Plot CNA segments.
plot_segments_multisample | Plot multisample cna data
plot_segment_size_distribution | Plot the length of clonal simple CNAs.
plot_smoothing | Plot smoothed and non-smoohted segments.
print.cnaqc | Print for class "cnaqc".
print.m_cnaqc | Print for class "m_cnaqc".
SBS | Augment SBS data for mutational signatures deconvolution
SBS_counts | Extract SBS count data
smooth_segments | Smooth simple clonal CNAs.
split_by_chromosome | Split a dataset by chromosome.
subsample | Randomly subsample mutations.
subset_by_minimum_CCF | Subset mutations by minimum CCF
subset_by_segment_karyotype | Subset by clonal segments.
subset_by_segment_minmutations | Retain clonal segments with minimum number of mutations.
subset_by_segment_totalcn | Subset clonal simple segments total copy number.
subset_snvs | Subset only SNVs.
wt_mutant_alleles | Compute WT and mutant alleles per gene