Man pages for Wedge-Oxford/dpclust
DPClust - An R package for subclonal reconstruction of tumours using sequencing data
| add.in.cn.as.single.snv | Function that adds copy number as a single SNV into a data... |
| add.in.cn.as.snv.cluster | Function that adds copy number as a series of SNVs into a... |
| add.in.indels | Add indels to an existing dataset |
| add.mutphasing | Add mutation phasing information to a dataset |
| add_removed_snvs | Add removed mutations back into the assignment table. SNVs... |
| append.dataset | Convenience function to append two datasets |
| assign_cnas_to_clusters | Assign CNA events to clusters using their pseudoSNV... |
| build_coassignment_prob_matrix_densities | Build a coassignment probability matrix using SNV specific... |
| build_coassignment_prob_matrix_preferences | Helper function that builds a mutation to mutation... |
| calc_cluster_conf_intervals | Calculate confidence intervals on the cluster location |
| calc_cluster_order_probs | Calculate for a pair of clusters whether a has a higher CCF... |
| create_pseudo_snv | Create a number of pseudo SNVs to represent a CNA and add... |
| DirichletProcessClustering | Main function to run subclonal reconstruction |
| do_uniform_sampling | Uniformly sample mutations |
| DPClust | Dirichlet Process Clustering of mutations |
| flatten_3d_to_2d | Helper function that flattens a 3D array into a 2D one |
| getClusterDensity | Obtain the mean density of each cluster. |
| get_cnas_cluster_probs | Use the Pseudo-SNV probabilities to obtain a probability of... |
| get.conflicting.indices | Returns a list of subclonal SNV indices that are conflicting... |
| get_data_avail_for_sampling | Function that returns the indices of data that is available... |
| getLocalOptima | Function that fetches the local optima from a density... |
| get_mutation_preferences | Get mutation preferences table given a density and cluster... |
| get_snv_assignment_ccfs | Fetch the CCFs of the clusters to which SNVs have been... |
| get_snv_ccf_assignmnent_density | Helper function that builds the a density over assignment... |
| load.cn.data | Load the CN input for a single sample (for now) This expects... |
| load.data | This function loads a series of data tables or VCFs into a... |
| load.indel.data | Load the indel input This expects a DP indel input file |
| make_advanced_params | Helper function to package advanced parameters - most of... |
| make_cna_params | Helper function to package CNA parameters - to be implemented |
| make_run_params | Helper function to package run parameters |
| make_sample_params | Helper function to package sample parameters |
| multiDimensionalClustering | Establish clusters and assign mutations for multi-dimensional... |
| mutation_assignment_em | Assign mutations for multi-dimensional clustering by adding... |
| oneDimensionalClustering | Identify clusters and assign mutations for 1-dimensional... |
| plot1D | Original plotting function: Creates the 1D density plot in... |
| plot1D_2 | ggplot2 based density figure that can show CNA-pseudo-SNVs... |
| plotAssignmentTable | Plot a table with the assignment counts |
| plotnD | Create a 2D plot for multi-dimensional clustering |
| read_gsdata_object | Helper function to read in the DP algorithm files |
| remove_mutations | Helper function to remove a set of mutations from a dataset... |
| remove_pseudo_snv_cna_clusters | Replace the pseudo SNV clusters that represent a CNA event... |
| RunDP | Main DPClust function that handles the various pipelines |
| sample_mutations | Sample a number of mutations from the dataset to reduce its... |
| unsample_mutations | Unsample a sampled dataset and expand clustering results with... |
| writeStandardFinalOutput | Function that stores the final output in a unified format on... |
