Man pages for Kalhor-Lab/QFM
Quantitative Fate Mapping with ICE-FASE and Phylotime
| add_edge_length | Add edge length to edge df |
| as.phylo.type_graph | Convert type graph to phylo object |
| calc_bsum | Compute BSUM or Colless index value |
| calculate_type_counts | Calculate the counts before next division |
| cells_to_edges | Convert cells to edge data.frame |
| cells_to_nodes | Convert cells to node data.frame |
| change_target_time | Change target time |
| check_n_identity | Compre if two strings are identical other than 'N' characters |
| collaspe_di | collaspe nodes below certain threshold |
| concat_mut_p | Concatenate two 'mut_p' (mutagenesis parameters) objects. |
| concat_mut_p_list | Concatenate a list of 'mut_p' (mutagenesis parameters)... |
| construct_true_lineage_multi | deprecated now (repplaced by mod2) deprecated but no mod2... |
| distribute_all_mut_counts | Distribute allele counts for all elements |
| distribute_mut_counts | Distribute mutant allele counts between two groups |
| edges_df_to_newick | Convert simplified edges df to phylo |
| generate_diff_outcome | Generate differentiation outcome matrix for type graph |
| generate_edge_df | Generate edge data.frame for type graph, getting edge lengths... |
| generate_mut_ids | Generate a batch of depth-1 mutante allele |
| generate_nonrecur_mut_ids | Generate a batch of non recurring depth-1 mutante allele |
| generate_recur_mut_ids | Generate a batch of recurring depth-1 mutant allele |
| get_cell_type_counts | current version of cell phylogeny model |
| get_edge_diff | ICE-FASE inference when topology has multifurcations |
| get_edge_len | get edge length statistics to distinguish between g0 and g1 |
| get_mut_duration | get overlaps of intervals using trick on IRanges TODO:... |
| get_next | extend out node to the next bifurcation in the lineage tree |
| get_node_mapping | get mapping of inferred progenitor states to true progenitor... |
| get_sampled_cells | Get sampled cells of at target time |
| get_sample_size | Get sample size of sim_history |
| get_target_time | Get target time from sim_history |
| get_true_size_mod2 | this function returns the incoming size as well as the... |
| get_t_total | deprecated function, used for somatic mutation get the total... |
| hello | Hello, World! |
| ice_fase | reconstructs phylogeny with phylotime, and infers... |
| impute_characters | Impute missing characters from cell allele matrix |
| initialize_mut_element_counter | Initialize the global mut_element counter for non-recurring... |
| initialize_mut_state | Initialize unmutated matrix for single cell model |
| initial_states_list | Make initial states list |
| init_mut_counts_list | Initialize mutant allele count list for bulk counting |
| is_non_decs | Check if a vector is non-decreasing |
| is_zero_range | Check if a vector is all the same value |
| make_gr_tr_data | mostly deprecated functions of ICE_FASE, replaced by... |
| make_heatmap_col | Make a color palette for Heatmap visualization |
| make_mut_element | Constructor for mutation parameter for a single element Only... |
| make_mut_param_by_rate | Make a mut_param by a sequence of mutation rates |
| make_mut_param_by_rate_rvec | Make a mut_param by a sequence of mutation rates and... |
| make_type_graph | Constructor for type graph |
| mutate_barcodes | Generate mutant allele for single cell mutation states |
| mutate_cells | Mutate the barcodes for cells object |
| mut_counts_total | Gives the counts for mut_counts_list |
| normalize_row | Normalize rows of a matrix to be the same sum 'm' |
| normalize_tree | Construct lineage tree from sim_history |
| num_gen_single_type | Given a single cell type, generate the number of generations... |
| phylotime | Phylotime for reconstructing time-scaled phylogeny based on... |
| plot_col_vec | Plot a color vector for visualization |
| plot_gr_data | plot ice_fase results |
| plot_legend | Plot legend on a new canvas given a ggplot object |
| plot_type_graph | Plot type graph using ggraph |
| push_pdf | Push a ggplot object to a PDF file |
| push_png | Push a ggplot object to a PNG file |
| rstoc | Round a number stochasticly, returns integer greater than or... |
| sample_all_mut_counts | Draw one sample of mutation counts for all elements |
| sample_all_mut_counts_gen | Draw one sample of the mutation counts after a number of... |
| sample_doublet_branch | the stochastic coal function sample the number of doublet... |
| sample_doublet_twotype | the asymmetric coal function |
| sample_mut_counts | Draw one sample of the mutation counts after some time |
| scale_counts | deprecated Assign counts based on total and fraction, rounded... |
| sim_history_to_edges | Convert sim_history to edges data.frame |
| sim_history_to_nodes | Convert sim_history to nodes data.frame |
| simplify_edges_df | Remove internal nodes with single daughter |
| subsample_all_mut_counts | Draw subsample of allele counts for all elements |
| subsample_mut_counts | Draw a subsample of mutant allele counts |
| subset_mut_p | Subset a 'mut_p' object to a number of its elements |
| white_col_mapper | Generate a 'white' color vector for plotting |
