Discovering genomic regions where methylation is strongly
associated with transcriptional activity
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Documentation for package ‘methodical’ version 1.3.0
Help Pages
| methodical-package | methodical: A one-stop shop for dealing with big DNA methylation datasets |
| .calculate_regions_intersections | Calculate the number of bases in the intersection of two GRanges objects |
| .chunk_regions | Split genomic regions into balanced chunks based on the number of methylation sites that they cover |
| .count_covered_bases | Calculate the number of unique bases covered by all regions in a GRanges object |
| .create_meth_rse_from_hdf5 | Create a RangedSummarizedExperiment for methylation values already deposited in HDF5 |
| .expand_transcript_ranges | Add regions upstream of TSS and downstream of TES to a GRangesList for transcripts |
| .find_tmrs_single | Find TSS-Proximal Methylation-Controlled Regulatory Sites (TMRs) |
| .make_meth_rse_setup | Perform setup for makeMethRSEFromBedgraphs or makeMethRSEFromArrayFiles |
| .split_bedgraph | Split data from a single methylation array files into chunks |
| .split_bedgraphs_into_chunks | Split data from bedGraph files into chunks |
| .split_meth_array_file | Split data from a single methylation array files into chunks |
| .split_meth_array_files_into_chunks | Split data from methylation array 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 |
| annotateGRanges | Annotate GRanges |
| 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 |
| correct_correlation_pvalues | Correct p-values for a list of methylation-transcription correlations results |
| createRandomRegions | Create a GRanges with random regions from a genome |
| expand_granges | Expand GRanges |
| 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. |
| findTMRs | Find TSS-Proximal Methylation-Controlled Regulatory Sites (TMRs) |
| hg38_cpgs_subset | hg38_cpgs_subset |
| infinium_450k_probe_granges_hg19 | infinium_450k_probe_granges_hg19 |
| kallistoIndex | Create an index file for running Kallisto |
| kallistoQuantify | Run kallisto on a set of FASTQ files and merge the results |
| liftoverMethRSE | Liftover rowRanges of a RangedSummarizedExperiment for methylation data from one genome build to another |
| makeMethRSEFromArrayFiles | Create a HDF5-backed RangedSummarizedExperiment for methylation values in array files |
| makeMethRSEFromBedgraphs | Create a HDF5-backed RangedSummarizedExperiment for methylation values in bedGraphs |
| maskRangesInRSE | Mask regions in a ranged summarized experiment |
| methodical | methodical: A one-stop shop for dealing with big DNA methylation datasets |
| methrixToRSE | Convert a Methrix object into a RangedSummarizedExperiment |
| plotMethodicalScores | Create plot of Methodical score values for methylation sites around a TSS |
| plotMethSiteCorCoefs | Plot the correlation coefficients for methylation sites within a region and an associated feature of interest |
| plotMethylationValues | Create a plot of methylation values for methylation sites in a 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 methylation 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 |
| sumTranscriptValuesForGenes | Combine the expression values of transcripts to get overall expression of their associated genes |
| 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 |
| TumourMethDatasets | TumourMethDatasets |