Man pages for CompEpigen/scMethrix
Fast and efficient summarization of single cell whole genome bisulfate data
| append_colData | Appends colData in an scMethrix object |
| benchmark_imputation | Evaluates imputations methods by NRMSE or AUC |
| binarize | Binarize an input value based on a 'threshold' |
| bin_granges | Bins each region in a 'GRanges' object into bins of specified... |
| bin_scMethrix | Bins the ranges of an 'scMethrix' object. |
| cast_datatable | Casts genomic regions into 'data.table' format |
| cast_granges | Casts genomic regions into 'GRanges' format |
| cluster_scMethrix | Generates a cluster object for an 'scMethrix' object |
| colbind | A faster version of cbind when trying to combine lists of... |
| collapse_samples | Collapses multiple samples into a single sample by group |
| convert_HDF5_scMethrix | Converts HDF5 'scMethrix' object to an in-memory 'scMethrix'... |
| convert_scMethrix | Converts an in-memory 'scMethrix' to an HDF5 'scMethrix' |
| dim_red_scMethrix | Reduces dimensionality (tSNE, UMAP, PCA, or custom) |
| dot-validateArg | Validates arguments. Allows partial matching. |
| dot-validateAssay | Validates an assay is in the object. Allows partial pattern. |
| dot-validateExp | Validates to see if object is a proper scMethrix object |
| dot-validateThreads | Validates the number of threads for the session. Windows can... |
| dot-validateValue | Validates numeric values based on some experession |
| export_beds | Exports all samples in an 'scMethrix' objects into individual... |
| export_bigwigs | Exports scMethrix object as bigWigs |
| export_bsseq | Convert 'scMethrix' to 'bsseq' object |
| export_methrix | Converts an 'scMethrix' object to methrix object |
| extract_CpGs | Extracts all CpGs from a genome |
| fill | Fills a vector with a specified 'fill' value |
| generate_random_subset | Generates a random subset of CpG sites |
| generate_training_set | Splits an scMethrix object into two for use as a training and... |
| generic_scMethrix_function | Function used only for inheritence for Roxygen2... |
| get_distance_matrix | Get the pair-wise distance matrix for an assay |
| get_matrix | Extract assays from an 'scMethrix' object |
| get_metadata_stats | Adds descriptive statistics to metadata columns in an... |
| get_palette | Getter for plot palette colors |
| get_region_summary | Extracts and summarizes methylation or coverage info by... |
| get_sample_name | Returns sample name derived from the input file name |
| get_shape | Getter for plot shapes. Shapes selected for optimal... |
| get_source_idx | Gets bedgraph column indexes from common pipeline output... |
| get_stats | Estimate descriptive statistics for each sample |
| has_cov | Checks if 'scMethrix' object has a coverage matrix |
| impute_by_melissa | Imputes the NA values of a 'scMethrix' object. |
| impute_regions | Generic imputation return function |
| is_h5 | Checks if 'scMethrix' object is an HDF5 object |
| liftover_CpGs | Converts from one reference to another via... |
| load_HDF5_scMethrix | Loads HDF5 'scMethrix' object |
| mask_by_coverage | Masks CpGs by coverage |
| mask_by_sample | Masks CpGs by cell count |
| mask_by_variance | Masks non-variable CpGs |
| mask_helper | Helper function for masking. All rows in row_idx will be set... |
| merge_scMethrix | Merges two 'scMethrix' objects by 'row' or 'col' |
| parse_source_idx | Subsets a given list of CpGs by another list of CpGs |
| plot_coverage | Coverage QC Plots |
| plot_density | Density Plot of beta-Values |
| plot_dim_red | Plot dimensionality reduction |
| plot_sparsity | Sparsity of sample inheritParams generic_plot_function |
| plot_stats | Plot descriptive statistics |
| plot_violin | Violin Plot for beta-Values |
| prepare_plot_data | Format 'scMethrix' matrix to long form data for plotting |
| read_bed_by_index | Parses BED files for methylation values using previously... |
| read_beds | Versatile BedGraph reader. |
| read_hdf5_data | Writes values from input BED files into an in-disk... |
| read_index | Parse BED files for unique genomic coordinates |
| read_mem_data | Writes values from input BED files into an in-memory 'matrix' |
| reduce_cpgs | Reduces a assay to a representative matrix |
| remove_assay | Removes an assay from an 'scMethrix' object |
| remove_uncovered | Remove loci that are uncovered across all samples |
| save_HDF5_scMethrix | Saves an HDF5 'scMethrix' object |
| scMethrix-class | Class scMethrix |
| scMethrix_data | Single cell methylome of murine neuronal cells |
| scMethrix_theme | Theme for ggplot |
| split_time | Outputs the split/lap/iteration time |
| split_vector | Splits a vector into list of vectors by 'chunk' or 'size' |
| start_time | Starts an internal stopwatch |
| stop_time | Stops an internal stopwatch and outputs overall time |
| subset_ref_cpgs | Subsets a given list of CpGs by another list of CpGs |
| subset_scMethrix | Subsets an 'scMethrix' object based on 'regions', 'contigs'... |
| transform_assay | Transforms an assay in an 'scMethrix' object. |
