Package index • qfm

All functions

add_edge_length(): Add edge length to edge df

as.phylo(<type_graph>): Convert type graph to phylo object

calculate_type_counts(): Calculate the counts before next division

calc_bsum(): Compute BSUM or Colless index value

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) objects.

construct_true_lineage_multi(): deprecated now (repplaced by mod2) deprecated but no mod2 available now

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 from laid out graph

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: dependes on IRanges

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 states

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 outgoing sizes

get_t_total(): deprecated function, used for somatic mutation get the total amount of time passed that the site could have mutated

hello(): Hello, World!

ice_fase(): reconstructs phylogeny with phylotime, and infers quantitative fate map with ice_fase

impute_characters(): Impute missing characters from cell allele matrix

initialize_mut_element_counter(): Initialize the global mut_element counter for non-recurring alleles

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 'ice_fase_mod1.R' some functions are still used for processing downstream results

make_heatmap_col(): Make a color palette for Heatmap visualization

make_mut_element(): Constructor for mutation parameter for a single element Only supports max_depth of 1

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 multinomial allele probabilities

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 it will divide until it reaches target time or differentiate

phylotime(): Phylotime for reconstructing time-scaled phylogeny based on lineage barcodes

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 equal to one.

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 generatioins

sample_doublet_branch(): the stochastic coal function sample the number of doublet branches when dividing n cells into 2*n cell

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 to integer Ensure that each category gets some minimum of counts Scale counts based on a factor, rounded to integer, counts must be at least 1

simplify_edges_df(): Remove internal nodes with single daughter

sim_history_to_edges(): Convert sim_history to edges data.frame

sim_history_to_nodes(): Convert sim_history to nodes data.frame

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