Man pages for lculibrk/Ploidetect
Ploidetect - Detection of tumour purity, aneuploidy, and copy number variation from whole genome sequnce data
| centromeres | Centromeres for hg19. |
| compute_responsibilities | Computes responsibilities for a gaussian mixture model with... |
| cosine_sim | Compute cosine similarity of two vectors |
| curate_segments | Merge noisy segments with their locally dominant segment |
| depth | Compute predicted depths based on coverage characteristics |
| gmm_em_fixed_var | Optimizes mean differential for a special case of gaussian... |
| gmm_em_only_var | Determines variance for a gaussian mixture model (GMM) given... |
| gmm_mad | Computes weighted median absolute deviations (MADs) for each... |
| load_ploidetect_data | Load data from Ploidetect's output |
| maf_gmm_fit | Fits a gaussian mixture-of-alleles model |
| map_noisy_segments | Map all segments within an interval to the dominant CN state |
| match_kde_height | Estimate variance by comparison to a density estimate |
| mixpdf | Generate the probability density function (pdf) of the... |
| mixpdf_function | Generate a function that outputs the probability density... |
| n50_segments | Compute the n50 length of vector of lengths |
| norm_lik | Likelihood function of a gaussian distribution |
| normpdf | Probability density function of a gaussian distribution |
| parametric_gmm_fit | Fits a gaussian mixture model with specified parameters to... |
| plot_ploidetect | Produce ploidetect-style plots for a copy number profile |
| props | Convert vector into probability distribution |
| rms | Compute the root-mean-squared (rms) deviation of a vector |
| table_vec | Return a vectorized counts table |
| tp_diffploidy | Compute tumour purity at a different ploidy |
| view_segments | Produce ploidetect-style plots for a copy number profile at... |
| zt | Z-score |
| zt_p | Standardized normal p-value |
