Man pages for caravagnalab/CNAqc
CNAqc - Copy Number Analysis quality check
| 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... |
| CCF | Extract CCF estimates. |
| chr_coordinates_GRCh38 | Coordinates for GRCh38 chromosomes. |
| chr_coordinates_hg19 | Coordinates for hg19 chromosomes. |
| CNA | Extract CNAs. |
| CNA_gene | Extract per-gene copy number status. |
| CNAqc-package | CNAqc: CNAqc - Copy Number Analysis quality check |
| 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... |
| gene_coordinates_GRCh38 | Coordinates for GRCh38 genes |
| gene_coordinates_hg19 | Coordinates for hg19 genes |
| get_drivers | Extract drivers data. |
| get_PASS_percentage | Returns percentage of passed segments |
| init | Creates a CNAqc object. |
| inspect_segment | Plot VAFs across chromosomes. |
| intogen_drivers | List of Intogen driver genes per tumour type. |
| Mutations | Extract mutations. |
| parse_Battenberg | Parse Battenberg calls. |
| pipe | Pipe operator |
| plot_arm_fragmentation | Plot the arm level fragmentation test. |
| plot_CCF | Plot the CCF estimates in the data. |
| plot.cnaqc | Plot for class "cnaqc". |
| 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_segment_size_distribution | Plot the length of clonal simple CNAs. |
| plot_smoothing | Plot smoothed and non-smoohted segments. |
| print.cnaqc | Print for class "cnaqc". |
| SBS | Augment SBS data for mutational signatures deconvolution |
| SBS_counts | Extract SBS count data |
| Sequenza_CNAqc | CNAqc-based purity-optimisation pipeline for Sequenza. |
| 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 |
