Package: methrix 1.27.0

Anand Mayakonda

methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Authors:Anand Mayakonda [aut, cre], Reka Toth [aut], Rajbir Batra [ctb], Clarissa Feuerstein-Akgöz [ctb], Joschka Hey [ctb], Maximilian Schönung [ctb], Pavlo Lutsik [ctb]

methrix_1.27.0.tar.gz
methrix_1.27.0.zip(r-4.7)methrix_1.27.0.zip(r-4.6)methrix_1.27.0.zip(r-4.5)
methrix_1.27.0.tgz(r-4.6-any)methrix_1.27.0.tgz(r-4.5-any)
methrix_1.27.0.tar.gz(r-4.7-any)methrix_1.27.0.tar.gz(r-4.6-any)
methrix_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methrix/json (API)

# Install 'methrix' in R:

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

Bug tracker:https://github.com/compepigen/methrix/issues

Datasets:

methrix_data - WGBS for colon cancer, chr21 and chr22

On BioConductor:methrix-1.27.0(bioc 3.24)methrix-1.26.0(bioc 3.23)

dnamethylation sequencing coverage bedgraph bioinformatics dna-methylation

7.56 score 36 stars 84 scripts 27 exports 77 dependencies

Last updated from:13c2ece168. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	435
linux-devel-x86_64	NOTE	673
source / vignettes	OK	629
linux-release-x86_64	NOTE	758
macos-release-arm64	NOTE	512
macos-oldrel-arm64	NOTE	409
windows-devel	NOTE	634
windows-release	NOTE	615
windows-oldrel	NOTE	547
wasm-release	OK	447

Exports:combine_methrix convert_HDF5_methrix convert_methrix coverage_filter extract_CPGs get_matrix get_region_summary get_stats load_HDF5_methrix mask_methrix methrix_pca methrix_report methrix2bsseq order_by_sd plot_coverage plot_density plot_pca plot_stats plot_violin read_bedgraphs region_filter remove_snps remove_uncovered save_HDF5_methrix subset_methrix write_bedgraphs write_bigwigs

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops BSgenome cigarillo cli codetools cpp11 crayon curl data.table DelayedArray DelayedMatrixStats dir.expiry farver filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable h5mread HDF5Array httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats mime openssl R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray sparseMatrixStats SummarizedExperiment sys vctrs viridisLite withr XML XVector yaml

Methrix tutorial

Rendered frommethrix.Rmdusingknitr::rmarkdown

Last update: 2020-10-23
Started: 2019-05-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Combine methrix objects	combine_methrix
Converts HDF5 methrix object to standard in-memory object.	convert_HDF5_methrix
Converts an in-memory object to an on-disk HDF5 object.	convert_methrix
Filter matrices by coverage	coverage_filter
Extracts all CpGs from a genome	extract_CPGs
Extract methylation or coverage matrices	get_matrix
Extract and summarize methylation or coverage info by regions of interest	get_region_summary
Estimate descriptive statistics	get_stats
Loads HDF5 methrix object	load_HDF5_methrix
Masks too high or too low coverage	mask_methrix
WGBS for colon cancer, chr21 and chr22	methrix_data
Principal Component Analysis	methrix_pca
Creates a detailed interative html summary report from Methrix object	methrix_report
Class methrix	methrix methrix-class
Convert 'methrix' to 'bsseq' object	methrix2bsseq
Order mathrix object by SD	order_by_sd
Coverage QC Plots	plot_coverage
Density Plot of beta-Values	plot_density
Plot PCA results	plot_pca
Plot descriptive statistics	plot_stats
Violin Plot for beta-Values	plot_violin
Versatile BedGraph reader.	read_bedgraphs
Filter matrices by region	region_filter
Removes CpG sites from the object if they overlap with common SNPs	remove_snps
Remove loci that are uncovered across all samples	remove_uncovered
Saves HDF5 methrix object	save_HDF5_methrix
Subsets 'methrix' object based on given conditions.	subset_methrix
Writes bedGraphs from methrix object	write_bedgraphs
Exports methrix object as bigWigs	write_bigwigs