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

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Documentation for package ‘flowGraph’ version 1.14.0

• 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.