Package: AlphaBeta 1.19.0

Yadollah Shahryary Dizaji

AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging.

Authors:Yadollah Shahryary Dizaji [cre, aut], Frank Johannes [aut], Rashmi Hazarika [aut]

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NEWS

# Install 'AlphaBeta' in R:

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

On BioConductor:AlphaBeta-1.19.0(bioc 3.20)AlphaBeta-1.18.0(bioc 3.19)

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

bioconductor-package

14 exports 0.71 score 85 dependencies 7 mentions

Last updated 2 months agofrom:1aaed3e2e0

Exports:ABneutral ABneutralSOMA ABnull ABplot ABselectMM ABselectMMSOMA ABselectUU ABselectUUSOMA BOOTmodel buildPedigree dMatrix FtestRSS plotPedigree rc.meth.lvl

Dependencies:askpass base64enc BH BiocParallel bslib cachem cli codetools colorspace cpp11 crosstalk curl data.table digest dplyr evaluate expm fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics ggplot2 glue gtable gtools highr htmltools htmlwidgets httr igraph isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme nloptr numDeriv openssl optimx pillar pkgconfig plotly pracma promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales snow stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

AlphaBeta

Y.Shahryary, Rashmi Hazarika, Frank Johannes

Rendered fromAlphaBeta.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-04-26
Started: 2019-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run Model with no selection (ABneutral)	ABneutral
Model with no selection (outneutral)	ABneutralSOMA
Run model that considers no accumulation of epimutations (ABnull)	ABnull
Plotting estimates	ABplot
Run model with selection against spontaneous gain of methylation (ABselectMM)	ABselectMM
Model with selection against spontaneous gain of methylation (outselectMM)	ABselectMMSOMA
Run model with selection against spontaneous loss of methylation (ABselectUU)	ABselectUU
Model with selection against spontaneous loss of methylation (outselectUU)	ABselectUUSOMA
Bootstrap analysis with the best model	BOOTmodel
Building Pedigree	buildPedigree
Constructing D-Matrices	dMatrix
Comparison of different models and selection of best model	FtestRSS
Plot Pedigree	plotPedigree
Calculating rc.Meth.lvl	rc.meth.lvl