Components analysis for multiple objects

Share:

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

1
2
3
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.