| check_package |
Check if a package is installed |
| forceReverse |
Force reversal of a subset of the ordering |
| human_bm |
Human gene symbols and positions |
| initialOrder |
Ordering the molecules/reads |
| methylscaper |
methylscaper |
| methyl_average_status |
Calculate the average methylation/accessibility status across all cells/molecules. |
| methyl_percent_sites |
Calculates the percentage of methylated cells/molecules per site |
| methyl_proportion |
Calculate the proportion of methylated bases for each cell/molecule |
| mouse_bm |
Mouse gene symbols and positions |
| plotSequence |
Generate Sequence Plot |
| prepSC |
Process single-cell data |
| reads_sm |
Example reads from single-molecule experiment |
| refineFunction |
Refinement |
| reformatSCE |
This is an internal function for now and a place-holder in case SingleCellExperiment may be used in the future. We may need to update this later. Assumes rownames are formatted like chr_pos and there are two assays. The assay names are 'methylation_met' for endogenous methylation and 'methylation_acc' for accessibility. |
| ref_seq |
Example reference sequence to align reads to from a single-molecule experiment |
| runAlign |
Align the single-molecule data |
| singlecell_subset |
Example preprocessed single-cell experiment subset |
| singlemolecule_example |
Example preprocessed single-molecule experiment |
| subsetSC |
Load in methylation data |
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