Package: bigmelon 1.39.0

Leonard C. Schalkwyk

bigmelon: Illumina methylation array analysis for large experiments

Methods for working with Illumina arrays using gdsfmt.

Authors:Tyler J. Gorrie-Stone [aut], Ayden Saffari [aut], Karim Malki [aut], Leonard C. Schalkwyk [cre, aut]

bigmelon_1.39.0.tar.gz
bigmelon_1.39.0.zip(r-4.7)bigmelon_1.39.0.zip(r-4.6)bigmelon_1.39.0.zip(r-4.5)
bigmelon_1.39.0.tgz(r-4.6-any)bigmelon_1.39.0.tgz(r-4.5-any)
bigmelon_1.39.0.tar.gz(r-4.7-any)bigmelon_1.39.0.tar.gz(r-4.6-any)
bigmelon_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bigmelon/json (API)

# Install 'bigmelon' in R:

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

Datasets:

cantaloupe - Small MethyLumi 450k data sets for testing
honeydew - Small MethyLumi 450k data sets for testing

On BioConductor:bigmelon-1.39.0(bioc 3.24)bigmelon-1.38.0(bioc 3.23)

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

dnamethylation microarray twochannel preprocessing qualitycontrol methylationarray dataimport cpgisland

5.41 score 37 scripts 7 mentions 83 exports 168 dependencies

Last updated from:2d036fd425. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	572
linux-devel-x86_64	WARNING	948
source / vignettes	OK	705
linux-release-x86_64	WARNING	888
macos-release-arm64	WARNING	443
macos-oldrel-arm64	WARNING	403
windows-devel	WARNING	604
windows-release	WARNING	619
windows-oldrel	WARNING	608
wasm-release	OK	533

Exports:[.gds.class [.gdsn.class app2gds backup.gdsn betaqn betas bigpepo bumphunterEngine.gdsn chainsaw colnames combo.gds computebeta.gds danen danen.gds danes danes.gds danet danet.gds dasen dasen.gds dasenrank daten1 daten1.gds daten2 daten2.gds db.gdsn dfsfit.gdsn dim.gds.class dim.gdsn.class dimnames.gds.class dimnames.gdsn.class dmrse dmrse_col dmrse_row es2gds estimateCellCounts.gds fData finalreport2gds findgdsobj fot fuks gds2mlumi gds2mset genki geotogds getHistory getpheno getquantiles getquantilesandranks getTrait handle iadd iadd2 idats2gds methylated nanes nanes.gds nanet nanet.gds nasen nasen.gds naten naten.gds newgds pData pfilter pfilter.gds prcomp.gds.class predictSex pvals pwod.gdsn QCmethylated QCrownames QCunmethylated qn.gdsn qual redirect.gds rownames seabi subSet swan tost unmethylated

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr evaluate farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options gdsfmt genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread HDF5Array highr hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig 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 ROC Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo 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 wateRmelon withr xfun XML xml2 xtable XVector yaml

The bigmelon Package

Rendered frombigmelon.Rnwusingutils::Sweave

Last update: 2018-10-14
Started: 2016-10-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Write large-scale Illumina array datasets to CoreArray Genomic Data Structure (GDS) data files for efficient storage, access, and modification.	bigmelon-package bigmelon
Append a MethyLumiSet object to a preexisting gds file	app2gds
Copy gds node to a backup folder within gds object	backup.gdsn
Bigmelon accessors	'[.gds.class' '[.gdsn.class' betas,gds.class-method bigmelon-accessors colnames,gds.class-method colnames,gdsn.class-method exprs,gds.class-method fData,gds.class-method fot fot,gds.class-method getHistory,gds.class-method methylated,gds.class-method pData,gds.class-method pvals,gds.class-method QCmethylated QCmethylated,gds.class-method QCrownames QCrownames,gds.class-method QCunmethylated QCunmethylated,gds.class-method rownames,gds.class-method rownames,gdsn.class-method unmethylated,gds.class-method
Bigmelon Quantile Normalization methods.	betaqn,gds.class-method danen,gds.class-method danen.gds danes,gds.class-method danes.gds danet,gds.class-method danet.gds dasen,gds.class-method dasen.gds daten1,gds.class-method daten1.gds daten2,gds.class-method daten2.gds db.gdsn dfsfit.gdsn nanes,gds.class-method nanes.gds nanet,gds.class-method nanet.gds nasen,gds.class-method nasen.gds naten,gds.class-method naten.gds qn.gdsn
tea.gds - description and validation for gds objects	bigPepo
Bumphunter using bigmelon	.getEstimate2 bumphunterEngine.gdsn
Small MethyLumi 450k data sets for testing	cantaloupe honeydew
Chainsaw - modify gds file by subsetting all nodes	chainsaw
Combine two different gds objects together	combo.gds
Dasen Quantile Normalization by storing ranks	computebeta.gds dasenrank
dim.gds.class S3 method returning dimensions of data represented by a gds file handle.	dim.gds.class
Coersion method for MethyLumiSet, RGChannelSet or MethylSet to CoreArray Genomic Data Structure (GDS) data file	es2gds
Cell Proportion Estimation using bigmelon	estimateCellCounts.gds getquantiles
Read finalreport files and convert to genomic data structure files	finalreport2gds
Convert Genomic Data Structure file to Methylumiset or Methylset object.	gds2mlumi gds2mset
Download data from GEO and convert it into a gdsfmt object	geotogds getpheno
Compute the quantiles and ranks for a given gdsn.node	.sortvector getquantilesandranks
Add data from Illumina IDAT files to a gds file.	iadd iadd2 idats2gds
Basic data filtering for Illumina methylation data in gds objects	pfilter,gds.class pfilter,gds.class-method pfilter.gds
Principal Component Analysis for high-dimensional data	prcomp, gds.class prcomp, gds.class-method prcomp.gds prcomp.gds.class
Probe-Wise Outlier Detection for DNA methylation data.	pwod, gds.class pwod, gdsn.class pwod.gdsn
Change the location of the paths for row and column names in a gds file.	redirect.gds
Functions imported from wateRmelon	dmrse,gds.class-method dmrse,gdsn.class-method dmrse_col,gds.class-method dmrse_col,gdsn.class-method dmrse_row,gds.class-method dmrse_row,gdsn.class-method genki,gds.class-method genki,gdsn.class-method predictSex predictSex,gds.class-method predictSex,gdsn.class-method qual,gdsn.class,gdsn.class-method seabi,gds.class-method wm-port