General
.switch to using BSSeq?
.Generalize to histone data? Show exampe with Roadmap data and RNA-seq
. Change meth sites from single position to whole palindormes? Check BSseq

methodical.R ! Revise if updating to also work with histone data

chunk_regions.R # Default is one core
.chunk_regions

rapid_cor_test.R
.rapidCorTest

meth_rse_functions.R ! Show examples for all in meth_rse vignette
.extractGRangesMethSiteValues # Check if redundant and rename get_values_overlapping_regions
.sampleMethSites ! Show example in working_with_meth_rse vignette with e.g. mouse for CpG islands, gene bodies, repeats
.liftoverMethRSE
.maskRangesInRSE 

plotting_functions.R
rangesRelativeToTSS ! Make non-exported
plotRegionValues
plotMethSiteCorCoefs ! Simplify to use code from plotRegionValues
plotTMRs Generalize to worj with other regions?
plotMethodicalScores ! Simplify to use code from plotRegionValues
annotatePlot

granges_manipulation.R
extractMethSitesFromGenome ! Check if redundant with 
.expand_granges ! Check if redundant with promoters?
.strandedDistance ! Make non-exported + plus check if any other function cab perform the same task?
extractMethSitesFromGenome ! Check if redundnat with 
rangesRelativeToTSS ! Make non-exported?
.count_covered_bases. # Used by calculate_regions_intersections. ! Remove from package?
calculate_regions_intersections # Used by annotateGRanges. ! Remove from package?
createRandomRegions ! Check if redundant with RegioneR

genome_annotation.R
.annotateGRanges ! Remove from package? 

object_documentation.R ! Check that all objects included

kallisto_quantify.R: ! Remove from package
.kallistoIndex
.kallistoQuantify
.sumTranscriptValuesForGenes
