Bayesian clustering and imputationa of single cell methylomes

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Documentation for package ‘Melissa’ version 1.18.0

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

Help Pages

.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_files	Impute/predict methylation files
impute_test_met	Impute/predict test 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