bigmelon: Illumina methylation array analysis for large experiments

Methods for working with Illumina arrays using gdsfmt.

Author
Tyler Gorrie-Stone, Ayden Saffari, Karim Malki, Leonard C Schalkwyk
Date of publication
None
Maintainer
Tyler Gorrie-Stone <tgorri@essex.ac.uk>
License
GPL-3
Version
1.0.0

View on Bioconductor

Man pages

app2gds
Append a MethyLumiSet object to a CoreArray Genomic Data...
backupGdsn
Copy gds node to a backup folder within gds object
bigmelon-accessors
Bigmelon accessors
bigmelon-internal
Internal bigmelon functions
bigmelon-normalization
Bigmelon Quantile Normalization methods.
bigmelon-package
Write large-scale Illumina array datasets to CoreArray...
cantaloupe
Small MethyLumi 450k data sets for testing
combogds
Combine two different gds objects.
es2gds
Coersion method for MethyLumiSet, RGChannelSet or MethylSet...
finalreport2gds
Read finalreport files and convert to genomic data structure...
gds2mlumi
Convert Genomic Data Structure file to Methylumiset or...
iadd
Add data from IDAT files for a single barcode to a gds file
pfiltergds
Basic data filtering for Illumina methylation data in gds...
prcompgdsn
Principal Component Analysis for high-dimensional data
pwodgdsn
Probe-Wise Outlier Detection
redirect
Change the location of file 'paths' for row and column names.
wm-port
Functions ported from wateRmelon

Files in this package

bigmelon/DESCRIPTION
bigmelon/NAMESPACE
bigmelon/NEWS
bigmelon/R
bigmelon/R/comboGds.R
bigmelon/R/dasenGds.R
bigmelon/R/dbGdsn.R
bigmelon/R/dfsfitGdsn.R
bigmelon/R/es2gds.R
bigmelon/R/gds2mlumi.R
bigmelon/R/gdsnclass_methods.R
bigmelon/R/inout.R
bigmelon/R/pfilterGds.R
bigmelon/R/prcompGdsn.R
bigmelon/R/pwodGdsn.R
bigmelon/R/qnGdsn.R
bigmelon/R/zzz.R
bigmelon/README.md
bigmelon/build
bigmelon/build/vignette.rds
bigmelon/data
bigmelon/data/cantaloupe.rda
bigmelon/data/honeydew.rda
bigmelon/inst
bigmelon/inst/doc
bigmelon/inst/doc/bigmelon.R
bigmelon/inst/doc/bigmelon.Rnw
bigmelon/inst/doc/bigmelon.pdf
bigmelon/inst/unitTests
bigmelon/inst/unitTests/test_internal.R
bigmelon/inst/unitTests/test_user.R
bigmelon/man
bigmelon/man/app2gds.Rd
bigmelon/man/backupGdsn.Rd
bigmelon/man/bigmelon-accessors.Rd
bigmelon/man/bigmelon-internal.Rd
bigmelon/man/bigmelon-normalization.Rd
bigmelon/man/bigmelon-package.Rd
bigmelon/man/cantaloupe.Rd
bigmelon/man/combogds.Rd
bigmelon/man/es2gds.Rd
bigmelon/man/finalreport2gds.Rd
bigmelon/man/gds2mlumi.Rd
bigmelon/man/iadd.Rd
bigmelon/man/pfiltergds.Rd
bigmelon/man/prcompgdsn.Rd
bigmelon/man/pwodgdsn.Rd
bigmelon/man/redirect.Rd
bigmelon/man/wm-port.Rd
bigmelon/tests
bigmelon/tests/runTests.R
bigmelon/vignettes
bigmelon/vignettes/bigmelon.Rnw
bigmelon/vignettes/logmemuse.pdf