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 1.0.2

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MultiDataSet-package MultiDataSet: Implementation of the BRGE's basic classes
add-rnaseq Method to add an expression RNA seq dataset to 'MultiDataSet'.
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_snps Method to add a slot of SNPs to 'MultiDataSet'.
add_snps-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
fData MultiDataSet instances
fData-method MultiDataSet instances
getMs Transforms beta values to M-values
getMs-method MethylationSet instances
length MultiDataSet instances
length-method MultiDataSet instances
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
pData MultiDataSet instances
pData-method MultiDataSet instances
prepareMethylationSet Generating a 'MethylationSet'
rowRanges MultiDataSet instances
rowRanges-method MultiDataSet instances
sampleNames-method MultiDataSet instances
[ MultiDataSet instances
[-method MultiDataSet instances
[[-method MultiDataSet instances