# Bayesian clustering and imputationa of single cell methylomes

## Documentation for package ‘Melissa’ version 1.3.0

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

## Help Pages

Melissa-package | 'Melissa': Bayesian clustering and imputation of single cell methylomes
.datatable.aware | 'Melissa': Bayesian clustering and imputation of single cell methylomes
binarise_files | Binarise CpG sites
cluster_ari | Compute clustering ARI
cluster_error | Compute clustering assignment error 'cluster_error' computes the clustering assignment error, i.e. the average number of incorrect cluster assignments: OE =sum_{n=1}^{N}(I(LT_{n} \neq LP_{n})) / N
create_melissa_data_obj | Create methylation regions for all cells
eval_cluster_performance | Evaluate clustering performance
eval_imputation_performance | Evaluate imputation performance
extract_y | Extract responses y
filter_by_coverage_across_cells | Filtering process prior to running Melissa
filter_by_cpg_coverage | Filtering process prior to running Melissa
filter_by_variability | Filtering process prior to running Melissa
filter_cpgs, | Filtering process prior to running Melissa
filter_regions | Filtering process prior to running Melissa
impute_met_state | Impute/predict methylation states
init_design_matrix | Initialise design matrices
log_sum_exp | Compute stable log-sum-exp
Melissa | 'Melissa': Bayesian clustering and imputation of single cell methylomes
melissa | Cluster and impute single cell methylomes using VB
melissa_cluster, | Cluster and impute single cell methylomes using VB
melissa_encode_dt | Synthetic ENCODE single cell methylation data
melissa_filter | Filtering process prior to running Melissa
melissa_gibbs | Gibbs sampling algorithm for Melissa model
melissa_impute, | Cluster and impute single cell methylomes using VB
melissa_synth_dt | Synthetic single cell methylation data
melissa_vb | Cluster and impute single cell methylomes using VB
partition_dataset | Partition synthetic dataset to training and test set
plot_melissa_profiles | Plot predictive methylaation profiles