Package: methodical 1.9.0

Richard Heery

methodical: Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Authors:Richard Heery [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methodical/json (API)

# Install 'methodical' in R:

install.packages('methodical', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/richardheery/methodical/issues

Datasets:

chr1_subset_hg38 - Chr1_subset_hg38
chr11_subset_hg38_cpgs - Chr11_subset_hg38_cpgs
chr4_subset_a_thal - Chr4_subset_a_thal
hg19_chr18_cpgs - Hg19_chr18_cpgs
hg38_cpg_islands - Hg38_cpg_islands
infinium_450k_probe_granges_hg19 - Infinium_450k_probe_granges_hg19
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

On BioConductor:methodical-1.9.0(bioc 3.24)methodical-1.8.0(bioc 3.23)

dnamethylation methylationarray transcription genomewideassociation software

3.86 score 40 scripts 311 downloads 24 exports 200 dependencies

Last updated from:f774c22d4d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	185
linux-devel	NOTE	478
source / vignettes	OK	316
linux-release	NOTE	497
macos-release	NOTE	291
macos-oldrel	NOTE	310
windows-devel	NOTE	325
windows-release	NOTE	312
windows-oldrel	NOTE	308
wasm-release	OK	196

Exports:annotatePlot calculateMethSiteTranscriptCors calculateRegionMethylationTranscriptCors calculateSmoothedMethodicalScores convert_rse_to_bsseq correct_correlation_pvalues expand_granges export_files_from_rse extractGRangesMethSiteValues extractMethSitesFromGenome findTMRs liftoverMethRSE makeMethRSEFromInputFiles maskRangesInRSE methrixToRSE plotMethodicalScores plotMethSiteCorCoefs plotRegionValues plotTMRs rangesRelativeToTSS rapidCorTest sampleMethSites strandedDistance summarizeRegionMethylation

Dependencies:abind AnnotationDbi AnnotationHub askpass assorthead base64enc beachmat BH Biobase BiocBaseUtils BiocCheck BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocStyle BiocVersion biocViews Biostrings bit bit64 bitops blob bookdown brew brio BSgenome bslib bsseq cachem callr cigarillo cli clipr codetools commonmark cowplot cpp11 crayon credentials curl data.table DBI dbplyr DelayedArray DelayedMatrixStats desc devtools diffobj digest dir.expiry downlit dplyr ellipsis evaluate ExperimentHub fansi farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges gert ggplot2 gitcreds glue graph gtable gtools h5mread HDF5Array highr htmltools htmlwidgets httpuv httr httr2 ini IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime miniUI openssl otel pak permute pillar pkgbuild pkgconfig pkgdown pkgload png praise prettyunits processx profvis promises ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs RBGL rcmdcheck RColorBrewer Rcpp RcppRoll RCurl rdtools remotes restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown roxygen2 rprojroot Rsamtools RSQLite rstudioapi rtracklayer RUnit rversions rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo sessioninfo shiny snow sourcetools SparseArray sparseMatrixStats statmod stringdist stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tinytex UCSC.utils urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun XML xml2 xopen xtable XVector yaml zip

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

Package: methodical 1.9.0

methodical: Discovering genomic regions where methylation is strongly associated with transcriptional activity

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