# Illumina methylation array analysis for large experiments

## Documentation for package ‘bigmelon’ version 1.31.1

- 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