.check_input_files      Check input files have the correct number of
                        columns specified and that columns seem to be
                        of correct type
.chunk_regions          Split genomic regions into balanced chunks
                        based on the number of methylation sites that
                        they cover
.collapse_strands       Combine values for stranded data
.create_meth_rse_from_hdf5
                        Create a RangedSummarizedExperiment for
                        methylation values already deposited in HDF5
.find_tmrs_single       Find TSS-Proximal Methylation-Controlled
                        Regulatory Sites (TMRs)
.make_meth_rse_setup    Perform setup for makeMethRSEFromInputFiles or
                        makeMethRSEFromArrayFiles
.set_meth_df_columns    Process a data.frame with methylation data so
                        that it contains the correct columns
.split_meth_file        Split data from a single input methylation file
                        into chunks
.split_meth_files_into_chunks
                        Split data from input methylation files into
                        chunks
.summarize_chunk_methylation
                        Summarize methylation values for regions in a
                        chunk
.test_tmrs              Find TMRs where smoothed methodical scores
                        exceed thresholds
.tss_correlations       Calculate meth site-transcript correlations for
                        given TSS
.tss_iterator           Create an iterator function for use with
                        bpiterate
.write_chunks_to_hdf5   Write chunks of data to a HDF5 sink
annotatePlot            Create a plot with genomic annotation for a
                        plot of values at methylation sites.
calculateMethSiteTranscriptCors
                        Calculate correlation between expression of
                        transcripts and methylation of sites
                        surrounding their TSS
calculateRegionMethylationTranscriptCors
                        Calculate the correlation values between the
                        methylation of genomic regions and the
                        expression of associated transcripts
calculateSmoothedMethodicalScores
                        Calculate methodical score and smooth it using
                        a exponential weighted moving average
chr11_subset_hg38_cpgs
                        chr11_subset_hg38_cpgs
chr1_subset_hg38        chr1_subset_hg38
chr4_subset_a_thal      chr4_subset_a_thal
convert_rse_to_bsseq    Convert a methylation RSE to a BSseq object
correct_correlation_pvalues
                        Correct p-values for a list of
                        methylation-transcription correlations results
expand_granges          Expand GRanges upstream and downstream
export_bedGraph_from_rse
                        Export values for a sample in a
                        RangedSummarizedExperiment as a bedGraph
extractGRangesMethSiteValues
                        Extract values for methylation sites
                        overlapping genomic regions from a methylation
                        RSE.
extractMethSitesFromGenome
                        Create a GRanges with methylation sites of
                        interest from a BSgenome or DNAStringSet
findTMRs                Find TSS-Proximal Methylation-Controlled
                        Regulatory Sites (TMRs)
hg19_chr18_cpgs         hg19_chr18_cpgs
hg38_cpg_islands        hg38_cpg_islands
infinium_450k_probe_granges_hg19
                        infinium_450k_probe_granges_hg19
liftoverMethRSE         Liftover rowRanges of a
                        RangedSummarizedExperiment for methylation data
                        from one genome build to another
makeMethRSEFromInputFiles
                        Create a HDF5-backed RangedSummarizedExperiment
                        for methylation values in meth_files
maskRangesInRSE         Mask regions in a ranged summarized experiment
methodical-package      methodical: A one-stop shop for dealing with
                        big DNA methylation datasets
methrixToRSE            Convert a Methrix object into a
                        RangedSummarizedExperiment
plotMethSiteCorCoefs    Plot the correlation coefficients for
                        methylation sites within a region and an
                        associated feature of interest
plotMethodicalScores    Create plot of Methodical score values for
                        methylation sites around a TSS
plotRegionValues        Create a scatter plot with smoothed curve for
                        values along adjacent loci in a genomic region
plotTMRs                Add TMRs to a methylation site value plot
rangesRelativeToTSS     Find locations of genomic regions relative to
                        transcription start sites.
rapidCorTest            Rapidly calculate the correlation and the
                        significance of pairs of columns from two
                        data.frames
sampleMethSites         Randomly sample sites from a methylation RSE.
strandedDistance        Calculate distances of query GRanges upstream
                        or downstream of subject GRanges
summarizeRegionMethylation
                        Summarize methylation of genomic regions within
                        samples
tubb6_correlation_plot
                        tubb6_correlation_plot
tubb6_cpg_meth_transcript_cors
                        tubb6_cpg_meth_transcript_cors
tubb6_meth_rse          tubb6_meth_rse
tubb6_tmrs              tubb6_tmrs
tubb6_transcript_counts
                        tubb6_transcript_counts
tubb6_tss               tubb6_tss
