Package: MethEvolSIM 0.3.0

MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

DNA methylation is an epigenetic modification involved in genomic stability, gene regulation, development and disease. DNA methylation occurs mainly through the addition of a methyl group to cytosines, for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine). Tissue-specific methylation patterns lead to genomic regions with different characteristic methylation levels. E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of expressed genes tend to be unmethylated. 'MethEvolSIM' is a model-based simulation software for the generation and modification of cytosine methylation patterns along a given tree, which can be a genealogy of cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree. The simulations are based on an extension of the model of Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of the methylation states at single cytosine positions as well as simultaneous changes of methylation frequencies in genomic structures like CpG islands.

Authors:Sara Castillo Vicente [aut, cre], Dirk Metzler [aut, ths]

MethEvolSIM_0.3.0.tar.gz
MethEvolSIM_0.3.0.zip(r-4.7-any)MethEvolSIM_0.3.0.zip(r-4.6-any)MethEvolSIM_0.3.0.zip(r-4.5-any)
MethEvolSIM_0.3.0.tgz(r-4.6-any)MethEvolSIM_0.3.0.tgz(r-4.5-any)
MethEvolSIM_0.3.0.tar.gz(r-4.7-any)MethEvolSIM_0.3.0.tar.gz(r-4.6-any)
MethEvolSIM_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MethEvolSIM/json (API)

# Install 'MethEvolSIM' in R:
install.packages('MethEvolSIM', repos = c('https://sarisworld.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.32 score 14 scripts 360 downloads 27 exports 6 dependencies

Last updated from:e4b141cbd0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK201
source / vignettesOK252
linux-releaseOK207
macos-releaseOK285
macos-oldrelOK268
windows-develOK198
windows-releaseOK146
windows-oldrelOK248
wasm-releaseOK105

Exports:categorize_islandGlbStcategorize_siteMethStcompare_CherryFreqscompute_fitchcompute_meanCor_icompute_meanCor_nicomputeFitch_islandGlbStcountSites_cherryMethDifffreqSites_cherryMethDiffget_cherryDistget_islandMeanFreqMget_islandMeanFreqPget_islandSDFreqMget_islandSDFreqPget_meanMeth_islandsget_nonislandMeanFreqMget_nonislandMeanFreqPget_nonislandSDFreqMget_nonislandSDFreqPget_parameterValuesget_siteFChange_cherrymean_CherryFreqsChange_imean_TreeFreqsChange_iMeanSiteFChange_cherrypValue_CherryFreqsChange_isimulate_evolDatasimulate_initialData

Dependencies:apedigestlatticenlmeR6Rcpp

CFTP Method
Introduction | Use examples | Convergence and Convergence Approximations | Visual Examples | Reproducibility | Workflow Requirements | Steps in the Workflow | References
Rendered fromCFTP_method-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-03-17
Started: 2025-03-17

Introduction to MethEvolSIM
A first example | Model parameters | Initial methylation state distribution | DNA methylation evolution processes | Island-wide events (IWEs) | Single-site events (SSEs) | Simulation Setup | Structural distribution of CpG sites | Parameter values | Simulation of DNA Methylation Data | Simulation of Initial Data | Exploration of Initial Data | Simulation of Data Evolution | References
Rendered fromintro-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-03-17
Started: 2024-04-19

Summary Statistics
Introduction | Frequency of Methylation States per Genomic Structure Type | Global Mean | Mean SD of Observed Frequencies per Structure Type at Tree Tips | Mean Correlation of a Central Segment of Methylation States per Genomic Structure Type | Comparison of tree tips | Mean Frequency of Methylation State Changes at Single Sites per Structure Type | Fitch Parsimony Estimate for Minimum Global Methylation State Changes at CpG Islands | Mean Number of Significant Methylation Frequency Changes per Island and Cherry | Mean Number of Significant Methylation Frequency Changes per Island Across All Tree Tips | References
Rendered fromsumstats-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-03-17
Started: 2025-03-17

Readme and manuals

Help Manual

Help pageTopics
Categorize Global States of CpG Islandscategorize_islandGlbSt
Categorize Methylation Frequencies Based on Thresholdscategorize_siteMethSt
cftpStepGeneratorcftpStepGenerator
combiStructureGeneratorcombiStructureGenerator
Compare Methylation Frequencies Between Two Tipscompare_CherryFreqs
Compute Fitch Parsimony for Methylation Categoriescompute_fitch
Compute the Mean Correlation of Methylation State in Islandscompute_meanCor_i
Compute the Mean Correlation of Methylation State in Non-islandscompute_meanCor_ni
Compute Fitch Parsimony for Global Methylation States at CpG IslandscomputeFitch_islandGlbSt
Count Methylation Statescount_upm
Count Methylation Differences Between Cherry PairscountSites_cherryMethDiff
Compute Methylation Frequency Differences Between Cherry PairsfreqSites_cherryMethDiff
Get Cherry Pair Distances from a Phylogenetic Treeget_cherryDist
Calculate the Mean Frequency of Methylated Sites in Islandsget_islandMeanFreqM
Calculate the Mean Frequency of Partially Methylated Sites in Islandsget_islandMeanFreqP
Calculate the Mean Standard Deviation of Methylated Sites in Islandsget_islandSDFreqM
Calculate the Mean Standard Deviation of Partially Methylated Sites in Islandsget_islandSDFreqP
Compute the Mean Methylation of CpG Islandsget_meanMeth_islands
Calculate the Mean Frequency of Methylated Sites in Non-Islandsget_nonislandMeanFreqM
Calculate the Mean Frequency of Partially Methylated Sites in Non-Islandsget_nonislandMeanFreqP
Calculate the Mean Standard Deviation of Methylated Sites in Non-Islandsget_nonislandSDFreqM
Calculate the Mean Standard Deviation of Partially Methylated Sites in Non-Islandsget_nonislandSDFreqP
Get Default Parameter Valuesget_parameterValues
Compute Site Frequency of Methylation Changes per Cherryget_siteFChange_cherry
Mean Number of Significant Methylation Frequency Changes per Island in Cherriesmean_CherryFreqsChange_i
Mean Number of Significant Frequency Changes per Island Across all Tree Tipsmean_TreeFreqsChange_i
Compute the Mean Site Frequency of Methylation Changes per CherryMeanSiteFChange_cherry
Compute p-Values for Methylation Frequency Changes in CherriespValue_CherryFreqsChange_i
Simulate Data Evolution along a Treesimulate_evolData
Simulate Initial Datasimulate_initialData
singleStructureGeneratorsingleStructureGenerator
treeMultiRegionSimulatortreeMultiRegionSimulator
Validate Structure of Input Data for Cherry Distance Computationvalidate_data_cherryDist
Validate Data Structure Across Tipsvalidate_dataAcrossTips
Validate Structure Indices for Island and Non-Island Datavalidate_structureIndices
Validate and Parse a Phylogenetic Treevalidate_tree