bigmelon: Illumina methylation array analysis for large experiments
Version 1.2.0

Methods for working with Illumina arrays using gdsfmt.

AuthorTyler J. Gorrie-Stone [cre, aut], Ayden Saffari [aut], Karim Malki [aut], Leonard C. Schalkwyk [aut]
Bioconductor views CpGIsland DNAMethylation DataImport MethylationArray Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerTyler J. Gorrie-Stone <tgorri@essex.ac.uk>
LicenseGPL-3
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bigmelon")

Getting started

Package overview
README.md

Popular man pages

app2gds: Append a MethyLumiSet object to a CoreArray Genomic Data...
backupGdsn: Copy gds node to a backup folder within gds object
bigmelon-internal: Internal bigmelon functions
bigmelon-normalization: Bigmelon Quantile Normalization methods.
ecc: Cell Proportion Estimation using bigmelon
es2gds: Coersion method for MethyLumiSet, RGChannelSet or MethylSet...
prcompgdsn: Principal Component Analysis for high-dimensional data
See all...

All man pages Function index File listing

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.
ecc: Cell Proportion Estimation using bigmelon
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...
GEOtoGDS: Download GEO data and pipe into a gdsfmt object
getquantilesandranks: Compute the quantiles and ranks for a given gdsn.node
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
rankednorm: Dasen Quantile Normalization by storing ranks
redirect: Change the location of file 'paths' for row and column names.
wm-port: Functions ported from wateRmelon

Functions

'[.gds.class' Man page
'[.gdsn.class' Man page
.sortvector Man page
QCmethylated Man page
QCmethylated,gds.class-method Man page
QCrownames Man page
QCrownames,gds.class-method Man page
QCunmethylated Man page
QCunmethylated,gds.class-method Man page
[.gds.class Man page
[.gdsn.class Man page
app2gds Man page Source code
backup.gdsn Man page Source code
betaqn,gds.class-method Man page
betas,gds.class-method Man page
bigmelon Man page
bigmelon-accessors Man page
bigmelon-internal Man page
bigmelon-package Man page
bmrownames Man page
bmrownames,gds.class-method Man page
cantaloupe Man page
colnames,gds.class-method Man page
colnames,gdsn.class-method Man page
combo.gds Man page Source code
computebeta.gds Man page Source code
danen,gds.class-method Man page
danen.gds Man page Source code
danes,gds.class-method Man page
danes.gds Man page Source code
danet,gds.class-method Man page
danet.gds Man page Source code
dasen,gds.class-method Man page
dasen.gds Man page Source code
dasen2 Man page
dasenrank Man page Source code
daten1,gds.class-method Man page
daten1.gds Man page Source code
daten2,gds.class-method Man page
daten2.gds Man page Source code
db.gdsn Man page Source code
design.qn.gdsn Man page
dfsfit.gdsn Man page Source code
dfsfit.gdsn.class.1 Man page
dmrse,gds.class-method Man page
dmrse,gdsn.class-method Man page
dmrse_col,gds.class-method Man page
dmrse_col,gdsn.class-method Man page
dmrse_row,gds.class-method Man page
dmrse_row,gdsn.class-method Man page
es2gds Man page Source code
estimateCellCounts.gds Man page Source code
exprs,gds.class-method Man page
fData,gds.class-method Man page
finalreport2gds Man page Source code
findgdsobj Man page Source code
fot Man page
fot,gds.class-method Man page
gds2mlumi Man page Source code
gds2mset Man page Source code
genki,gds.class-method Man page
genki,gdsn.class-method Man page
geotogds Man page Source code
getHistory,gds.class-method Man page
getTrait Man page Source code
getpheno Man page Source code
getquantiles Man page Source code
getquantilesandranks Man page Source code
handle Man page Source code
honeydew Man page
iadd Man page Source code
iadd2 Man page Source code
impose Man page Source code
methylated,gds.class-method Man page
nanes,gds.class-method Man page
nanes.gds Man page Source code
nanet,gds.class-method Man page
nanet.gds Man page Source code
nasen,gds.class-method Man page
nasen.gds Man page Source code
naten,gds.class-method Man page
naten.gds Man page Source code
newgds Man page Source code
normalizeQuantiles.gdsn.class Man page
normalizeQuantiles2 Man page Source code
onLoad Source code
pData,gds.class-method Man page
pfilter,gds.class Man page
pfilter,gds.class-method Man page
pfilter.gds Man page Source code
prcomp, gds.class Man page
prcomp, gds.class-method Man page
prcomp.gds Man page
prcomp.gds.class Man page Source code
pvals,gds.class-method Man page
pwod, gds.class Man page
pwod, gdsn.class Man page
pwod.gdsn Man page Source code
qn.gdsn Man page Source code
qual,gdsn.class,gdsn.class-method Man page
redirect.gds Man page Source code
rownames,gds.class-method Man page
rownames,gdsn.class-method Man page
seabi,gds.class-method Man page
sortvector Source code
subSet Man page
subSet,gds.class-method Man page
unmethylated,gds.class-method Man page
wm-port Man page
zot Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GEOtoGDS.R
R/comboGds.R
R/dasenGds.R
R/dbGdsn.R
R/dfsfitGdsn.R
R/ecc.gdsn.R
R/es2gds.R
R/gds2mlumi.R
R/gdsnclass_methods.R
R/inout.R
R/pfilterGds.R
R/prcompGdsn.R
R/pwodGdsn.R
R/qnGdsn.R
R/ranknorm.R
R/zzz.R
README.md
build
build/vignette.rds
data
data/cantaloupe.rda
data/honeydew.rda
inst
inst/doc
inst/doc/bigmelon.R
inst/doc/bigmelon.Rnw
inst/doc/bigmelon.pdf
inst/unitTests
inst/unitTests/test_internal.R
inst/unitTests/test_user.R
man
man/GEOtoGDS.Rd
man/app2gds.Rd
man/backupGdsn.Rd
man/bigmelon-accessors.Rd
man/bigmelon-internal.Rd
man/bigmelon-normalization.Rd
man/bigmelon-package.Rd
man/cantaloupe.Rd
man/combogds.Rd
man/ecc.Rd
man/es2gds.Rd
man/finalreport2gds.Rd
man/gds2mlumi.Rd
man/getquantilesandranks.Rd
man/iadd.Rd
man/pfiltergds.Rd
man/prcompgdsn.Rd
man/pwodgdsn.Rd
man/rankednorm.Rd
man/redirect.Rd
man/wm-port.Rd
tests
tests/runTests.R
vignettes
vignettes/bigmelon.Rnw
vignettes/logmemuse.pdf
bigmelon documentation built on May 20, 2017, 9:28 p.m.

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