Package: EMAS 0.2.2

EMAS: Epigenome-Wide Mediation Analysis Study

DNA methylation is essential for human, and environment can change the DNA methylation and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide. For more information on the methods we used, please see the following references: Tingley, D. (2014) <doi:10.18637/jss.v059.i05>, Turner, S. D. (2018) <doi:10.21105/joss.00731>, Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.

Authors:Xiuquan Nie [aut, cph, cre], Mengyi Wang [ctb, rev], Weihong Chen [fnd]

EMAS_0.2.2.tar.gz
EMAS_0.2.2.zip(r-4.5)EMAS_0.2.2.zip(r-4.4)EMAS_0.2.2.zip(r-4.3)
EMAS_0.2.2.tgz(r-4.4-any)EMAS_0.2.2.tgz(r-4.3-any)
EMAS_0.2.2.tar.gz(r-4.5-noble)EMAS_0.2.2.tar.gz(r-4.4-noble)
EMAS_0.2.2.tgz(r-4.4-emscripten)EMAS_0.2.2.tgz(r-4.3-emscripten)
EMAS.pdf |EMAS.html✨
EMAS/json (API)

# Install 'EMAS' in R:

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

Datasets:

E.result - An 'Emas' results data.
Mvalue - A M-value matrix for 221 participants
data.m - A data for 221 participants

On CRAN:

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

4 exports 0.00 score 190 dependencies 214 downloads

Last updated 2 years agofrom:31172f224d. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 12 2024
R-4.5-win	NOTE	Sep 12 2024
R-4.5-linux	NOTE	Sep 12 2024
R-4.4-win	NOTE	Sep 12 2024
R-4.4-mac	NOTE	Sep 12 2024
R-4.3-win	OK	Aug 13 2024
R-4.3-mac	OK	Aug 13 2024

Exports:Emas EMAS.manhattan Emas.parallel EMAS.volcano

Dependencies:abind annotate AnnotationDbi askpass backports base64 base64enc beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot bslib bumphunter cachem calibrate checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gridExtra gtable HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b4.hg19 illuminaio IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lavaan lifecycle limma lme4 locfit lpSolve magrittr MASS Matrix MatrixGenerics matrixStats mclust mediation memoise mgcv mime minfi minqa mnormt multilevel multtest munsell mvtnorm nlme nloptr nnet nor1mix numDeriv openssl pbivnorm pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr qqman quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer rvest S4Arrays S4Vectors sandwich sass scales scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

Help page	Topics
A data for 221 participants	data.m
An 'Emas' results data.	E.result
Epigenome-Wide Mediation Analysis Study	Emas
Plotting the manhattan plot from the EMAS results	EMAS.manhattan
Epigenome-Wide Mediation Analysis Study: Parallel multiple mediation model	Emas.parallel
Plotting the volcano plot from the EMAS results	EMAS.volcano
A M-value matrix for 221 participants	Mvalue

Package: EMAS 0.2.2

EMAS: Epigenome-Wide Mediation Analysis Study

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)