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MultiDataSet (version 1.0.2)

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

Description

Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet. MultiDataSet is designed for integrating multi omics data sets and MethylationSet to contain normalized methylation data. These package contains base classes for MEAL and rexposome packages.

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Version

Version

1.0.2

License

file LICENSE

Maintainer

Carlos Ruiz

Last Published

February 15th, 2017

Functions in MultiDataSet (1.0.2)

chrNumToChar

Convert chr numbers to chr strings
add_rnaseq

Method to add an expression RNA seq dataset to MultiDataSet.
checkProbes

Filter MethylationSet probes
checkSamples

Modify a MethylationSet to only contain common samples
add_snps

Method to add a slot of SNPs to MultiDataSet.
MultiDataSet

MultiDataSet: Implementation of the BRGE's basic classes
prepareMethylationSet

Generating a MethylationSet
commonSamples

Method to select samples that are present in all datasets.
add_methy

Method to add a slot of methylation to MultiDataSet.
add_genexp

Method to add an expression microarray dataset to MultiDataSet.
MultiDataSet-class

MultiDataSet instances
commonIds

Get the name of the ids common to all datasets
MethylationSet

MethylationSet instances
add_rse

Method to add a RangedSummarizedExperiment to MultiDataSet.
getMs

Transforms beta values to M-values
add_eset

Method to add an eSet to MultiDataSet.