# Visualization of Methylation Data

## Documentation for package ‘methylscaper’ version 1.0.0

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

## Help Pages

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