Discovering genomic regions where methylation is strongly
associated with transcriptional activity
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Documentation for package ‘methodical’ version 1.8.0
Help Pages
| methodical-package | methodical: A one-stop shop for dealing with big DNA methylation datasets |
| .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 | 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 |
| 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 |