Man pages for eyzhao/SignIT
What the Package Does (One Line, Title Case)
| all_snv_mutation_types | Gets a list of the standard 96 mutation types used in SNV... |
| base_complement | Returns the complementary sequence for a set of strings |
| collapse_mutation_types | Collapses mutation types of G>N and A>N mutations into C>N... |
| collapse_signatures_by_bleed | Collapse signatures using bleed information |
| collapse_signatures_by_bleed_all_solutions | Collapse signatures using bleed information |
| compute_population_bic | Bayesian Information Criterion for Population Models |
| compute_population_model_log_likelihood | Log Likelihood of Population Model |
| compute_population_signatures_bic | Bayesian Information Criterion for Population Signatures |
| compute_population_signatures_log_likelihood | Log Likelihood of Population Signatures Model |
| compute_population_signatures_waic | Watanabe-Akaike Information Criterion for Population... |
| compute_signatures_waic | Watanabe-Akaike Information Criterion for Signatures |
| get_density_mode | Convenience function for estimating the mode of dataset's... |
| get_exposure_pairwise_correlations | Pairwise correlation coefficients between signatures |
| get_exposures | Compute the MCMC sample space of exposure vectors |
| get_exposure_summary_table | Creates a summary table of exposure statistics |
| get_os | Gets the OS name |
| get_population_parameter_estimates | Point estimates for population Stan model output |
| get_populations | SignIT population model without mutation signatures |
| get_population_signatures | SignIT-Pop inference of populations and signatures |
| get_reference_signatures | Retrieves built-in reference mutation signature sets |
| get_signature_bleed_graph | Graph Representing Signature Bleed Relationships |
| get_signature_names | Parse Signature Names from Reference Signatures |
| get_snv_mutation_type | Given chromosome, position, reference, and altered allele... |
| get_trinucleotide | Gets the trinucleotide context for a set of genomic... |
| get_vaf_correction | Computes the VAF correction factor for a table of mutations |
| map_phi_to_population | Population Index Mapper |
| map_phi_to_signature | Signature Index Mapper |
| map_population_signatures | Maps Population Signature Parameters to their Signatures and... |
| mcmc_exposures_as_matrix | MCMC Exposures to Matrix |
| mutations_to_catalog | Given chromosome, position, reference, and altered allele... |
| mutation_types_match | Check Whether Mutation Types Match |
| normalize_reference_signatures | Normalization of reference signatures. |
| parse_stan_output | Stan Output Parser |
| plot_bleed_interactions | Creates a circular plot with links between signatures that... |
| plot_exposure_chain | Plot the MCMC chains for the signature exposure solutions |
| plot_exposure_posteriors | Plot the signature exposure posterior distributions |
| plot_exposure_posteriors_bleed | Plot the signature exposure posterior distribution along with... |
| plot_nnls_solution | Plots a simple NNLS solution |
| plot_population_signatures | Plot Population Signatures |
| plot_signature_pairwise_bleed | Plots pairwise correlations between signatures in MCMC... |
| plot_two_signature_hexplot | Plots a hexplot between two signatures |
| reference_signatures_as_matrix | Convert reference signatures to matrix |
| reverse_factor_levels | Reverse Factor Levels |
| reverse_factor_ranks | Reverse Factor Ranks |
| rotate_x_axis_labels | Rotates the x axis labels 90 degrees in ggplot graphs. |
| select_n_populations | Automatic Model Selection for Number of Populations |
| signature_present | Determine Presence or Absence of Signatures |
| SignIT-package | The 'SignIT' package. |
| stitch_mutation_types | Given a set of substitutions and trinucleotides, merge into... |
| subset_reference_signatures | Automatic subsetting of reference mutation signatures |
| summarise_population_signatures | Summarise Population Signatures |
| trim_signature_names | Trims the names of mutation signatures |
