# Identifying differential cell populations in flow cytometry data accounting for marker frequency

## Documentation for package ‘flowGraph’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cell_type_layers | Determines the layer on which a phenotype resides.
extract_markers | Extracts markers from cell population phenotypes
fg_add_feature | Adds a feature.
fg_add_summary | Adds a feature summary.
fg_clean_phen | Reformats phenotype
fg_clear_features | Clears all featuresin a flowGraph object.
fg_clear_summary | Removes all summary statistics.
fg_data_fca | fg_data_fca
fg_data_pos2 | fg_data_pos2
fg_data_pos30 | fg_data_pos30
fg_extract_phenotypes | Extracts a set of phenotypes from a flowGraph object.
fg_extract_raw | Clears all features and feature summaries in a flowGraph object.
fg_extract_samples | Extracts a set of samples from a flowGraph object.
fg_feat_cumsum | Converts cell counts into cumulated cell counts.
fg_feat_edge_prop | Generates the proportion edge feature.
fg_feat_edge_specenr | Generates the SpecEnr edge feature.
fg_feat_mean_class | Normalizes all features for class.
fg_feat_node_prop | Generates the proportion node feature.
fg_feat_node_specenr | Generates the SpecEnr node feature.
fg_get_feature | Retrieves a feature matrix.
fg_get_feature_desc | Retrieves and/or recalculates a feature description table.
fg_get_feature_means | Retrieves feature summaries.
fg_get_graph | Retrieves a graph list from a given flowGraph object.
fg_get_markers | Retrieves the markers from a given flowGraph object.
fg_get_meta | Retrieves sample meta.
fg_get_summary | Retrieves a summary statistic.
fg_get_summary_desc | Retrieves a feature summary description table.
fg_get_summary_index | Retrieves the index of the requested summary.
fg_get_summary_tables | Retrieves a table containing all node or edge summary statistics.
fg_gsub_ids | Replace sample id's.
fg_gsub_markers | Replace marker names.
fg_load | Load a flowGraph object from a specified folder path.
fg_merge | Merges two flowGraph objects together.
fg_merge_samples | Merges the samples from two flowGraph objects.
fg_plot | Creates a cell hierarchy plot.
fg_plot_box | Creates a boxplot of the values of one node/edge
fg_plot_pVSdiff | Creates a p value vs feature difference plot
fg_plot_qq | Creates a QQ plot of a summary statistic.
fg_replace_meta | Replaces sample meta.
fg_rm_feature | Removes a feature.
fg_rm_summary | Removes a feature summary.
fg_save | Saves flowGraph object to a specified path.
fg_save_plots | Saves numerous plots for all summary statistics to a folder.
fg_set_layout | Determines cell hierarchy layout.
fg_summary | Calculates feature summary statistics.
flowGraph | flowGraph object constructor.
flowGraph-class | 'flowGraph': A class for storing cell count feature values for the Phenotype class.
flowGraphSubset | flowGraph object constructor.
flowGraphSubset_summary_adjust | Default for flowGraphSubset's summary_adjust
flowGraphSubset_summary_pars | Default for flowGraphSubset's summary_pars
fpurrr_map | Wrapper for map
get_child | Gets child populations of given cell populations
get_eprop | Gets edge proportions of a given edge matrix
get_paren | Gets parent populations of given cell populations
get_phen_list | Creates edge lists.
get_phen_meta | Genrates phenotype meta data.
ggdf | Prepares a given node and edge graph list for plotting.
loop_ind_f | Prepares parallel loop indices.
mean_diff | Normalizes matrix values by class.
ms_create | Calcuate SpecEnr from proportion and expected proportion
ms_psig | Determines which phenotypes are statistically significant
plot_gr | Plots a cell hierarchy.
set_layout_graph | Determines cell hierarchy layout.
show-method | 'flowGraph': A class for storing cell count feature values for the Phenotype class.
summary_table | Summarizes a numeric matrix.
test_c | Converts input into a significance test function
time_output | Outputs elapsed time.
tstr | Formats time into string.