Illumina methylation array analysis for large experiments


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Documentation for package ‘bigmelon’ version 1.33.0

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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