omicsCompAnalysis: Components analysis for multiple objects

In llrs/STATegRa: Classes and methods for multi-omics data integration

Description

This function performs a components analysis of object wise omics data to understand the mechanisms that underlay all the data blocks under study (common mechanisms) and the mechanisms underlying each of the data block independently (distinctive mechanisms). This analysis include both, the preprocessing of data and the components analysis by using three different methodologies.

Usage

omicsCompAnalysis(Input, Names, method, Rcommon, Rspecific, 
                         convThres=1e-10, maxIter=600, center=FALSE, 
                         scale=FALSE, weight=FALSE)

Arguments

Input	List of ExpressionSet objects, one for each block of data.
Names	Character vector giving names for each Input object.
method	Method to use for analysis (either "DISCOSCA", "JIVE", or "O2PLS").
Rcommon	Number of common components between all blocks
Rspecific	Vector giving number of unique components for each input block
convThres	Stop criteria for convergence
maxIter	Maximum number of iterations
center	Character (or FALSE) specifying which (if any) centering will be applied before analysis. Choices are "PERBLOCKS" (each block separately) or "ALLBLOCKS" (all data together).
scale	Character (or FALSE) specifying which (if any) scaling will be applied before analysis. Choices are "PERBLOCKS" (each block separately) or "ALLBLOCKS" (all data together).
weight	Logical indicating whether weighting is to be done.

Value

An object of class caClass-class.

Author(s)

Patricia Sebastian Leon

Examples

data("STATegRa_S3")
B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,
pDataDescr=c("classname"))
B2 <- createOmicsExpressionSet(Data=Block2.PCA,
                               pData=ed.PCA,pDataDescr=c("classname"))
# Omics components analysis
discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)
jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                             method="JIVE",Rcommon=2,Rspecific=c(2,2),
                             center=TRUE,scale=TRUE,weight=TRUE)
o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="O2PLS",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.