Table 3 Workflow modules

downloadRepositoryData

Downloads data from an online repository

importMicroarrayData

Imports raw microarray data from Affymetrix and Illumina arrays

importProcessedData

Imports processed RNA, SNP, methylation and protein data

processMicroarrayData

Pre-processes microarray data

processSequencingData

Pre-processes sequencing data

processMassSpecData

Pre-processes mass spectrometry data

integrateAssays

Integrates several datasets into one

performFactorAnalysis

Performs factor analysis by matrix factorization

performHypothesisTest

Performs hypothesis testing

performLinearModeling

Performs generalized linear modeling with snpStats

performOmicsModeling

Performs modeling with limma, DMRcate or edgeR depending on the input object