Package: MAGAR 1.21.0

Michael Scherer

MAGAR: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Authors:Michael Scherer [cre, aut]

MAGAR_1.21.0.tar.gz
MAGAR_1.21.0.zip(r-4.7)MAGAR_1.21.0.zip(r-4.6)MAGAR_1.21.0.zip(r-4.5)
MAGAR_1.21.0.tgz(r-4.6-any)MAGAR_1.21.0.tgz(r-4.5-any)
MAGAR_1.21.0.tar.gz(r-4.7-any)MAGAR_1.21.0.tar.gz(r-4.6-any)
MAGAR_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MAGAR/json (API)

# Install 'MAGAR' in R:

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

Bug tracker:https://github.com/mpiicomputationalepigenetics/magar/issues

On BioConductor:MAGAR-1.21.0(bioc 3.24)MAGAR-1.20.0(bioc 3.23)

regression epigenetics dnamethylation snp geneticvariability methylationarray microarray cpgisland methylseq sequencing mrnamicroarray preprocessing copynumbervariation twochannel immunooncology differentialmethylation batcheffect qualitycontrol dataimport network clustering graphandnetwork

4.30 score 4 scripts 1 mentions 40 exports 193 dependencies

Last updated from:a893c77495. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	372
linux-devel-x86_64	NOTE	682
source / vignettes	OK	541
linux-release-x86_64	NOTE	686
macos-release-arm64	NOTE	463
macos-oldrel-arm64	NOTE	360
windows-devel	NOTE	564
windows-release	NOTE	601
windows-oldrel	NOTE	550
wasm-release	OK	348

Exports:computeCorrelationBlocks doImport doMethQTL doMethQTLChromosome filterPval getAnno getCorrelationBlocks getGeno getMethData getOverlappingQTL getOverlapUniverse getPheno getResult getResultGWASMap getSamples getSpecificQTL imputeMeth joinMethQTLResult loadMethQTLInput loadMethQTLResult overlapInputs overlapQTLs qtlAnnotationEnrichment qtlBaseSubstitutionEnrichment qtlDistanceScatterplot qtlGetOption qtlJSON2options qtlManhattanPlot qtlOptions2JSON qtlPlotBaseSubstitution qtlPlotClusterSize qtlPlotSNPCpGInteraction qtlSetOption qtlTFBSMotifEnrichment qtlUpsetPlot qtlUpSetPlotCorBlocks qtlUpSetPlotTagCpGs qtlVennPlot saveMethQTLInput saveMethQTLResult

Dependencies:abind affyio annotate AnnotationDbi argparse askpass base64 beanplot BH bigassertr bigparallelr bigstatsr Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem caTools cigarillo cli clipr cluster codetools cowplot cpp11 crayon crlmm curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doParallel doRNG dotCall64 dplyr ellipse farver fastmap FDb.InfiniumMethylation.hg19 ff fields filelock findpython flock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gplots gridExtra gtable gtools h5mread HDF5Array hms httr httr2 igraph illuminaio impute IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr maps MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mime minfi multtest mvtnorm nlme nor1mix oligoClasses openssl org.Hs.eg.db parallelly pillar pkgconfig plyr png preprocessCore prettyunits progress ps purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl Rhtslib rjson rlang rmio RnBeads RnBeads.hg19 RnBeads.hg38 rngtools Rsamtools RSpectra RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo siggenes snow snpStats spam SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils UpSetR utf8 vctrs VGAM viridisLite vroom withr XML xml2 xtable XVector yaml

MAGAR: Methylation-Aware Genotype Association in R

Rendered fromMAGAR.Rmdusingknitr::rmarkdown

Last update: 2021-10-20
Started: 2020-09-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
computeCorrelationBlocks	computeCorrelationBlocks
doImport	doImport
doMethQTL	doMethQTL
doMethQTLChromosome	doMethQTLChromosome
filterPval	filterPval filterPval,MethQTLResult-method
getAnno	getAnno getAnno,methQTL-method getAnno,MethQTLInput-method getAnno,MethQTLResult-method
getCorrelationBlocks	getCorrelationBlocks getCorrelationBlocks,MethQTLResult-method
getGeno	getGeno getGeno,methQTL-method getGeno,MethQTLInput-method
getMethData	getMethData getMethData,methQTL-method getMethData,MethQTLInput-method
getOverlappingQTL	getOverlappingQTL
getOverlapUniverse	getOverlapUniverse
getPheno	getPheno getPheno,methQTL-method getPheno,MethQTLInput-method
getResult	getResult getResult,MethQTLResult-method
getResultGWASMap	getResultGWASMap getResultGWASMap,MethQTLResult-method
getSamples	getSamples getSamples,methQTL-method getSamples,MethQTLInput-method
getSpecificQTL	getSpecificQTL
imputeMeth	imputeMeth imputeMeth,methQTL-method imputeMeth,MethQTLInput-method
joinMethQTLResult	joinMethQTLResult
loadMethQTLInput	loadMethQTLInput
loadMethQTLResult	loadMethQTLResult
MethQTLInput-class	MethQTLInput-class
MethQTLResult-class	MethQTLResult-class
overlapInputs	overlapInputs
overlapQTLs	overlapQTLs
options.R	QTL.OPTIONS
qtlAnnotationEnrichment	qtlAnnotationEnrichment
qtlBaseSubstitutionEnrichment	qtlBaseSubstitutionEnrichment
qtlDistanceScatterplot	qtlDistanceScatterplot
qtlGetOption Print the value of the global option	qtlGetOption
qtlJSON2options	qtlJSON2options
qtlManhattanPlot	qtlManhattanPlot
qtlOptions2JSON	qtlOptions2JSON
qtlPlotBaseSubstitution	qtlPlotBaseSubstitution
qtlPlotClusterSize	qtlPlotClusterSize
qtlPlotSNPCpGInteraction	qtlPlotSNPCpGInteraction
qtlSetOption	qtlSetOption
qtlTFBSMotifEnrichment	qtlTFBSMotifEnrichment
qtlUpsetPlot	qtlUpsetPlot
qtlUpSetPlotCorBlocks	qtlUpSetPlotCorBlocks
qtlUpSetPlotTagCpGs	qtlUpSetPlotTagCpGs
qtlVennPlot	qtlVennPlot
saveMethQTLInput	saveMethQTLInput saveMethQTLInput,methQTL-method saveMethQTLInput,MethQTLInput-method
saveMethQTLResult	saveMethQTLResult saveMethQTLResult,methQTL-method saveMethQTLResult,MethQTLResult-method