Illumina methylation array analysis for large experiments

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Documentation for package ‘bigmelon’ version 1.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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