omicsCompAnalysis

0th

Percentile

Components analysis for multiple objects

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.

Aliases
  • omicsCompAnalysis
  • omicsCompAnalysis,list,character,character,numeric,numeric-method
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)
Documentation reproduced from package STATegRa, version 1.6.2, License: GPL-2

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