_pkgdown.yml

template:
  params:
    bootswatch: spacelab
reference: 
- title: "BED input functions"
- contents:
  - read_beds
  - read_index
  - read_bed_by_index
  - read_hdf5_data
  - read_mem_data
  - subset_ref_cpgs
  - get_sample_name
  - parse_source_idx
  - get_source_idx
- title: "Base object and data"
- contents:
  - scMethrix-class
  - scMethrix_data
- subtitle: "Object getters"
- contents:
  - is_h5
  - has_cov
- title: "scMethrix base operations"
- subtitle: "Save/load and conversion"
- contents:
  - save_HDF5_scMethrix
  - load_HDF5_scMethrix
  - convert_HDF5_scMethrix
  - convert_scMethrix
  - convert_to_methrix
  - export_bed
- subtitle: "Assay retrieval"
- contents:
  - remove_assay
  - get_matrix
- subtitle: "Operations"
- contents:
  - merge_scMethrix
  - subset_scMethrix
  - mask_by_sample
  - mask_by_coverage
  - mask_by_variance
  - remove_uncovered
- subtitle: "Statistics"
- contents:
  - get_stats
  - get_region_summary
  - get_metadata_stats
- title: "scMethrix transformations"
- subtitle: "Assay transform"
- contents:
  - transform_assay
  - bin_scMethrix
  - binarize
- subtitle: "Imputation"
- contents:
  - impute_by_melissa
  - impute_regions
  - generate_training_set
  - generate_random_subset
- subtitle: "Dimensionality Reduction"
- contents:
  - dim_red_scMethrix
  - reduce_cpgs
- subtitle: "Clustering"
- contents:
  - get_distance_matrix
  - cluster_scMethrix
- title: "Plotting"
- contents: 
  - prepare_plot_data
  - plot_violin
  - plot_density
  - plot_coverage
  - plot_sparsity
  - plot_stats
  - plot_dim_red
  - get_palette
  - get_shape
  - benchmark_imputation
  - scMethrix_theme
- title: "Misc functions"
- subtitle: "GRanges/List"
- contents:
  - bin_granges
  - cast_granges
  - split_granges
  - split_vector
- subtitle: "Timer"
- contents:
  - start_time
  - split_time
  - stop_time