Visualization of Methylation Data

Documentation for package ‘methylscaper’ version 1.0.1

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