Package: missMethyl 1.41.0

Belinda Phipson

missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Authors:Belinda Phipson and Jovana Maksimovic

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NEWS

# Install 'missMethyl' in R:

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

On BioConductor:missMethyl-1.41.0(bioc 3.21)missMethyl-1.40.0(bioc 3.20)

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

normalization dnamethylation methylationarray genomicvariation geneticvariability differentialmethylation genesetenrichment

7.74 score 4 packages 319 scripts 1.8k downloads 54 mentions 18 exports 160 dependencies

Last updated 2 months agofrom:9006ed418b. Checks:OK: 1 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	WARNING	Nov 29 2024
R-4.5-linux	WARNING	Nov 29 2024
R-4.4-win	WARNING	Nov 29 2024
R-4.4-mac	WARNING	Nov 29 2024

Exports:contrasts.varFit densityByProbeType getAdj getINCs getLeveneResiduals getMappedEntrezIDs gometh goregion gsameth gsaregion gsaseq RUVadj RUVfit SWAN topGSA topRUV topVar varFit

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH BiasedUrn Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi farver fastmap FDb.InfiniumMethylation.hg19 foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue GO.db gridExtra gtable HDF5Array hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest munsell nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer ruv rvest S4Arrays S4Vectors scales scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Belinda Phipson and Jovana Maksimovic

Rendered frommissMethyl.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-05-15
Started: 2016-09-23

Help page	Topics
Introduction to the missMethyl package	missMethyl-package missMethyl
Compute contrasts for a varFit object.	contrasts.varFit
Plot the beta value distributions of the Infinium I and II probe types relative to the overall beta value distribution.	densityByProbeType
Extract values adjusted for unwanted variation by RUVm	getAdj
Extract intensity data for Illumina negative controls found on 450k or EPIC arrays.	getINCs
Obtain Levene residuals	getLeveneResiduals
Get mapped Entrez Gene IDs from CpG probe names	getMappedEntrezIDs
Gene ontology testing for Ilumina methylation array data	gometh
Gene ontology testing of DMRs for Ilumina methylation array data	goregion
Generalised gene set testing for Illumina's methylation array data	gsameth
Generalised gene set testing for Illumina's methylation array data	gsaregion
Generalised gene set testing for RNA-seq data	gsaseq
RUV adjust	RUVadj
Remove unwanted variation when testing for differential methylation	RUVfit
Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips	SWAN SWAN.default SWAN.MethyLumiSet SWAN.RGChannelSet
Get table of top 20 enriched pathways	topGSA
Table of top-ranked differentially methylated CpGs obatained from a differential methylation analysis using RUV	topRUV
Table of top-ranked differentially variable CpGs	topVar
Testing for differential variability	varFit varFit.default varFit.DGEList varFit.MethylSet

Package: missMethyl 1.41.0

missMethyl: Analysing Illumina HumanMethylation BeadChip Data

missMethyl: Analysing Illumina HumanMethylation BeadChip Data

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