Illumina methylation array analysis for large experiments


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Documentation for package ‘bigmelon’ version 1.0.0

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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
app2gds Append a MethyLumiSet object to a CoreArray Genomic Data Structure (GDS) data 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
cantaloupe Small MethyLumi 450k data sets for testing
colnames-method Bigmelon accessors
combo.gds Combine two different gds objects.
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.
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.
design.qn.gdsn Bigmelon Quantile Normalization methods.
dfsfit.gdsn Bigmelon Quantile Normalization methods.
dmrse-method Functions ported from wateRmelon
dmrse_col-method Functions ported from wateRmelon
dmrse_row-method Functions ported from wateRmelon
es2gds Coersion method for MethyLumiSet, RGChannelSet or MethylSet to CoreArray Genomic Data Structure (GDS) data file
exprs-method Bigmelon accessors
fData-method Bigmelon accessors
finalreport2gds Read finalreport files and convert to genomic data structure files
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 ported from wateRmelon
getHistory-method Bigmelon accessors
honeydew Small MethyLumi 450k data sets for testing
iadd Add data from IDAT files for a single barcode to a gds file
iadd2 Add data from IDAT files for a single barcode 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, gdsn.class Principal Component Analysis for high-dimensional data
prcomp-method Principal Component Analysis for high-dimensional data
prcomp.gdsn Principal Component Analysis for high-dimensional data
prcomp.gdsn.class Principal Component Analysis for high-dimensional data
pvals-method Bigmelon accessors
pwod, gds.class Probe-Wise Outlier Detection
pwod, gdsn.class Probe-Wise Outlier Detection
pwod.gdsn Probe-Wise Outlier Detection
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 ported from wateRmelon
redirect.gds Change the location of file 'paths' for row and column names.
rownames-method Bigmelon accessors
seabi-method Functions ported from wateRmelon
unmethylated-method Bigmelon accessors
wm-port Functions ported from wateRmelon