Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet


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Documentation for package ‘MultiDataSet’ version 1.4.0

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MultiDataSet-package MultiDataSet: Implementation of the BRGE's basic classes
add_eset Method to add an 'eSet' to 'MultiDataSet'.
add_eset-method MultiDataSet instances
add_genexp Method to add an expression microarray dataset to 'MultiDataSet'.
add_genexp-method MultiDataSet instances
add_methy Method to add a slot of methylation to 'MultiDataSet'.
add_methy-method MultiDataSet instances
add_rnaseq Method to add an expression RNA seq dataset to 'MultiDataSet'.
add_rnaseq-method MultiDataSet instances
add_rse Method to add a 'RangedSummarizedExperiment' to 'MultiDataSet'.
add_rse-method MultiDataSet instances
add_se Method to add a 'SummarizedExperiment' to 'MultiDataSet'.
add_se-method MultiDataSet instances
add_snps Method to add a slot of SNPs to 'MultiDataSet'.
add_snps-method MultiDataSet instances
add_table Method to add a 'matrix' to 'MultiDataSet'.
add_table-method MultiDataSet instances
as.list MultiDataSet instances
as.list-method MultiDataSet instances
assayData MultiDataSet instances
assayData-method MultiDataSet instances
betas MethylationSet instances
betas-method MethylationSet instances
checkProbes Filter 'MethylationSet' probes
checkProbes-method MethylationSet instances
checkSamples Modify a 'MethylationSet' to only contain common samples
checkSamples-method MethylationSet instances
chrNumToChar Convert chr numbers to chr strings
commonIds Get the name of the ids common to all datasets
commonIds-method MultiDataSet instances
commonSamples Method to select samples that are present in all datasets.
commonSamples-method MultiDataSet instances
createMultiDataSet MultiDataSet instances
dims MultiDataSet instances
dims-method MultiDataSet instances
fData MultiDataSet instances
fData-method MultiDataSet instances
featureData MultiDataSet instances
featureData-method MultiDataSet instances
getMs Transforms beta values to M-values
getMs-method MethylationSet instances
length MultiDataSet instances
length-method MultiDataSet instances
mae2mds Convert a 'MultiAssayExperiment' to a 'MultiDataSet'
mds2mae Convert a 'MultiDataSet' to a 'MultiAssayExperiment'
MethylationSet MethylationSet instances
methylationSet MethylationSet instances
MethylationSet-class MethylationSet instances
MethylationSet-methods MethylationSet instances
MultiDataSet MultiDataSet: Implementation of the BRGE's basic classes
MultiDataSet-class MultiDataSet instances
MultiDataSet-methods MultiDataSet instances
MultiDataSet-methods, MultiDataSet instances
names MultiDataSet instances
names-method MultiDataSet instances
ncols MultiDataSet instances
ncols-method MultiDataSet instances
nrows MultiDataSet instances
nrows-method MultiDataSet instances
pData MultiDataSet instances
pData-method MultiDataSet instances
phenoData MultiDataSet instances
phenoData-method MultiDataSet instances
rowRanges MultiDataSet instances
rowRanges-method MultiDataSet instances
rowRangesElements Get the name of the datasets that have rowRanges
rowRangesElements-method MultiDataSet instances
sampleNames-method MultiDataSet instances
subset-method MultiDataSet instances
w_iclusterplus Apply iClusterPlus clustering method to a MultiDataSet object
w_iclusterplus-method MultiDataSet instances
w_mcia Apply mcia integration method to a MultiDataSet object
w_mcia-method MultiDataSet instances
[ MultiDataSet instances
[-method MultiDataSet instances
[[-method MultiDataSet instances