Package index • FastCCCR

Core Analysis Functions

Main functions for CCC analysis

fastccc(): Simplified FastCCC Function

fastccc_cauchy(): FastCCC with Cauchy Combination

statistical_analysis_method(): FastCCC Single Method

cluster_markers_method(): Cluster Markers Method

create_significant_df(): Create Significant Interactions DataFrame

core: Core Functions for FastCCCR

Reference-Based Inference

Functions for building and using reference panels

build_reference(): Build Reference Panel

infer_query(): Infer Query Using Reference

load_reference_config(): Load Reference Config

build-reference: Reference Building Functions

infer-query: Query Inference Functions

Distribution Operations

Statistical distribution classes and functions

Distribution: Distribution Class for FastCCCR

create_distribution(): Create Distribution from Samples

get_pvalue(): Get p-value from Distribution

get_threshold(): Get threshold from Distribution (for significance)

get_minimum_distribution(): Get Minimum Distribution

get_pmf_from_digit_samples(): Get PMF Array from Digitized Samples

get_average_distribution(): Get Average Distribution

combine_complex_distribution_dt(): Combine Complex Distribution

dist-complex: Complex Distribution Functions

dist-iid-set: IID Set Distribution Functions

dist-lr: L-R Distribution and P-value Functions

Score Calculation

Functions for expression score computation

calculate_cluster_mean(): Calculate Cluster Mean Expression

calculate_cluster_percents(): Calculate Cluster Expression Percentages

calculate_cluster_quantile(): Calculate Cluster Quantile Expression

calculate_interactions_strength(): Calculate Interaction Strengths

combine_complex_distribution(): Combine Complex Distribution

analyze_interactions_percents(): Analyze Interaction Percentages

score: Score Calculation Functions for FastCCCR

P-value Computation

Functions for statistical inference

calculate_cluster_mean_distribution(): Calculate Cluster Mean Distribution

calculate_cluster_quantile_distribution(): Calculate Cluster Quantile Distribution

calculate_interactions_pvalue(): Calculate Interaction P-values

check_interactions_by_DEG(): Check Interactions by DEG

cauchy_combine(): Cauchy Combination of P-values

cauchy_combine_files(): Cauchy Combine from Files

cauchy_combine_with_stat(): Cauchy Combine with Statistic

cauchy-combine: Cauchy Combination Functions

Data Preprocessing

Functions for data loading and preprocessing

get_input_data(): Get Input Data from Seurat Object

get_interactions(): Get Interactions from Database

get_count_data(): Get Count Data Only

get_input_data_from_files(): Load Data from Files

data-preprocess: Data Preprocessing Functions for FastCCCR

Visualization

Plotting functions

plot_ccc_network(): Plot CCC Network

plot_ccc_heatmap(): Plot CCC Heatmap

plot_ccc_chord(): Plot CCC Chord Diagram

get_network_data(): Get Network Data

get_strength_network_data(): Get Strength Network Data

visualize: Visualization Functions for FastCCCR

C++ Functions

Low-level C++ implementations

calculate_cluster_means_cpp(): Calculate cluster means (vectorized)

calculate_cluster_percents_cpp(): Calculate cluster expression percentages

calculate_cluster_quantiles_cpp(): Calculate cluster quantiles (vectorized)

calculate_interaction_strengths_cpp(): Calculate interaction strengths (vectorized)

cauchy_combine_cpp(): Cauchy combination of p-values

digitize_transform_cpp(): Digitize transform for rank-based analysis

fast_histogram_cpp(): Fast histogram for PMF computation

fft_convolve_cpp(): FFT Convolution

get_minimum_distribution_cpp(): Minimum Distribution

get_pvalues_from_pmf_cpp(): Calculate P-values from PMF (vectorized)

multiply_distributions_cpp(): Multiply Distributions

sum_distributions_cpp(): Sum Distributions (for average)

Package

Package documentation

FastCCCR-package FastCCCR: FastCCCR: Fast Cell-Cell Communication Analysis

utils: FastCCCR Utility Functions