Man pages for adamwaring/ClusterBurden
Rare variant association utilising burden and positional information.
| annotate_with_gnomad_freqs | Annotate a dataset with GnomAD frequencies |
| BIN_test | Split data into bins and carry out a two-sample... |
| BIN_test_WES | Calculate a p-values from the BIN-test across the whole-exome |
| burden_test | Carry out a Fisher's exact test |
| burden_test_WES | Calculate Fisher's-exact p-values across the whole-exome |
| canon_txs | Canonical transcripts used in this package |
| clinvar_cases | ClinVAR variants |
| ClusterBurden_WES | ClusterBurden test for burden and position of rare-missense... |
| collect_example_cases | Make example cases based on ClinVAR and gnomAD data |
| collect_gnomad_controls | Automatically get controls for BIN-test and ClusterBurden... |
| color_vector | Personal colour palette |
| combine_ps | Combine p-values |
| econtrols | Control group - GnomAD exomes v2 |
| econtrols_nonpass | GnomAD exomes v2 variants that did not pass filters - for... |
| exome_cov | Coverage file for GnomAD exomes at gene-level |
| find_genes | Select a subset of genes to use in an WES analysis |
| findRanges | Find contiguous ranges of values in a vector of integers |
| format_coverage | Format coverage files from genome positions (chrom, pos) to... |
| gcontrols | Control group - GnomAD genomes v2 |
| gcontrols_nonpass | GnomAD genomes v2 variants that did not pass filters - for... |
| gene_locations | Genomic coordinates of all canonical genes |
| genome_cov | Coverage file for GnomAD genomes at a gene-level |
| get_residue_position | Extract amino acid residue position from HGVS protein... |
| grmap_reduced | Map between genome position and protein position in canonical... |
| manhattan | A Manhattan plot for p-values derived from a ClusterBurden... |
| nresidues | Length (in residues) of all canonical proteins |
| plot_distribs | Plot the distributions of case and control variant residues |
| plot_features | Plot sequence features such as domains alongside... |
| plot_residuals | Plot for chi-squared residuals |
| plot_signif_distribs | Plot the distributions of case and control variant residues... |
| remove_uncovered_residues | Exclude residue positions from a dataset based on coverage... |
| seq_features | Sequences features for all proteins downloaded from Uniprot |
| x10_gnomad | Proportion of samples with at least x10 for genes in GnomAD... |
