Package: bigmelon 1.33.0

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]

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

Peer review:

Datasets:
  • cantaloupe - Small MethyLumi 450k data sets for testing
  • honeydew - Small MethyLumi 450k data sets for testing

On BioConductor:bigmelon-1.33.0(bioc 3.21)bigmelon-1.32.0(bioc 3.20)

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

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarraydataimportcpgisland

5.69 score 28 scripts 310 downloads 7 mentions 83 exports 164 dependencies

Last updated 2 months agofrom:9e460f88b8. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winWARNINGNov 29 2024
R-4.5-linuxWARNINGNov 29 2024
R-4.4-winWARNINGNov 29 2024
R-4.4-macWARNINGNov 29 2024
R-4.3-winWARNINGNov 29 2024
R-4.3-macWARNINGNov 29 2024

Exports:[.gds.class[.gdsn.classapp2gdsbackup.gdsnbetaqnbetasbigpepobumphunterEngine.gdsnchainsawcolnamescombo.gdscomputebeta.gdsdanendanen.gdsdanesdanes.gdsdanetdanet.gdsdasendasen.gdsdasenrankdaten1daten1.gdsdaten2daten2.gdsdb.gdsndfsfit.gdsndim.gds.classdim.gdsn.classdimnames.gds.classdimnames.gdsn.classdmrsedmrse_coldmrse_rowes2gdsestimateCellCounts.gdsfDatafinalreport2gdsfindgdsobjfotfuksgds2mlumigds2msetgenkigeotogdsgetHistorygetphenogetquantilesgetquantilesandranksgetTraithandleiaddiadd2idats2gdsmethylatednanesnanes.gdsnanetnanet.gdsnasennasen.gdsnatennaten.gdsnewgdspDatapfilterpfilter.gdsprcomp.gds.classpredictSexpvalspwod.gdsnQCmethylatedQCrownamesQCunmethylatedqn.gdsnqualredirect.gdsrownamesseabisubSetswantostunmethylated

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrevaluatefansifarverfastmapFDb.InfiniumMethylation.hg19foreachformatRfutile.loggerfutile.optionsgdsfmtgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestmunsellnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryamlzlibbioc

The bigmelon Package

Rendered frombigmelon.Rnwusingutils::Sweaveon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 fileapp2gds
Copy gds node to a backup folder within gds objectbackup.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 objectsbigPepo
Bumphunter using bigmelon.getEstimate2 bumphunterEngine.gdsn
Small MethyLumi 450k data sets for testingcantaloupe honeydew
Chainsaw - modify gds file by subsetting all nodeschainsaw
Combine two different gds objects togethercombo.gds
Dasen Quantile Normalization by storing rankscomputebeta.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 filees2gds
Cell Proportion Estimation using bigmelonestimateCellCounts.gds getquantiles
Read finalreport files and convert to genomic data structure filesfinalreport2gds
Convert Genomic Data Structure file to Methylumiset or Methylset object.gds2mlumi gds2mset
Download data from GEO and convert it into a gdsfmt objectgeotogds 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 objectspfilter,gds.class pfilter,gds.class-method pfilter.gds
Principal Component Analysis for high-dimensional dataprcomp, 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 wateRmelondmrse,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