# Inferring Cell-Specific Gene Regulatory Network

## Documentation for package ‘inferCSN’ version 1.1.7

- DESCRIPTION file.

## Help Pages

inferCSN-package | _*inferCSN*_: *infer*ring *C*ell-*S*pecific gene regulatory *N*etwork
%ss% | Value selection operator
as_matrix | Convert sparse matrix into dense matrix
calculate_accuracy | Calculate Accuracy
calculate_auc | Calculate AUC Metrics
calculate_auprc | Calculate AUPRC Metric
calculate_auroc | Calculate AUROC Metric
calculate_f1 | Calculate F1 Score
calculate_gene_rank | Rank TFs and genes in network
calculate_ji | Calculate Jaccard Index
calculate_metrics | Calculate Network Prediction Performance Metrics
calculate_precision | Calculate Precision Metric
calculate_recall | Calculate Recall Metric
calculate_si | Calculate Set Intersection
check_sparsity | Check sparsity of matrix
coef.srm | Extracts a specific solution in the regularization path
coef.srm_cv | Extracts a specific solution in the regularization path
example_ground_truth | Example ground truth data
example_matrix | Example matrix data
example_meta_data | Example meta data
filter_sort_matrix | Filter and sort matrix
fit_srm | Sparse regression model
inferCSN | *infer*ring *C*ell-*S*pecific gene regulatory *N*etwork
inferCSN-method | *infer*ring *C*ell-*S*pecific gene regulatory *N*etwork
log_message | Print diagnostic message
matrix_to_table | Switch matrix to network table
meta_cells | Detection of metacells from single-cell gene expression matrix
network_format | Format network table
network_sift | Sifting network
normalization | Normalize numeric vector
parallelize_fun | Parallelize a function
pearson_correlation | Correlation and covariance calculation for sparse matrix
plot_coefficient | Plot coefficients
plot_coefficients | Plot coefficients for multiple targets
plot_contrast_networks | Plot contrast networks
plot_dynamic_networks | Plot dynamic networks
plot_edges_comparison | Network Edge Comparison Visualization
plot_embedding | Plot embedding
plot_histogram | Plot histogram
plot_network_heatmap | Plot network heatmap
plot_scatter | Plot expression data in a scatter plot
plot_static_networks | Plot dynamic networks
predict.srm | Predicts response for a given sample
predict.srm_cv | Predicts response for a given sample
print.srm | Prints a summary of 'sparse_regression'
print.srm_cv | Prints a summary of 'sparse_regression'
r_square | R^2 (coefficient of determination)
simulate_sparse_matrix | Generate a simulated sparse matrix for single-cell data testing
single_network | Construct network for single target gene
sparse_cor | Safe correlation function which returns a sparse matrix without missing values
sparse_cov_cor | Fast correlation and covariance calcualtion for sparse matrices
sparse_regression | Fit a sparse regression model
split_indices | Split indices.
subsampling | Subsampling function
table_to_matrix | Switch network table to matrix
weight_sift | Weight sift