STATegRa (version 1.0.0)

getVAF: Retrieve information about the VAF obtained using omicsCompAnalysis from an caClass-class

Description

Generic function to retrieve loadings (common and distinctive) obtained in the omicsCompAnalysis from an caClass-class

Usage

getVAF(x, part=NULL, block=NULL)

Arguments

x

caClass-class object. If only this parameter is specified loadings for common and distinctive part are diplayed

part

Character indicating if VAF for "common" or "distinctive" part has to be displayed. If the method is DISCO-SCA, another option, "cross", indicating the associated error due to the rotation is allowed

block

Character indicating the block of data whose VAF has to be returned. It can be specified by using the position of the block ("1" or "2") or the name assigned to this block in the caClass-class object. If it is NULL both VAFs are displayed

Value

By default, a list with VAF associated to both parts (common and distinctive). If any parameter is specified, the selected information is displayed.

Details

It is important to note that in the case of O2PLS method, it is not possible to calculate the VAF because the components are not orthogonal

See Also

omicsCompAnalysis, caClass-class

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
res <- omicsCompAnalysis(Input=list(B1, B2), Names=c("expr", "mirna"),
                         method="DISCOSCA", Rcommon=2, Rspecific=c(2, 2),
                         center=TRUE, scale=TRUE, weight=TRUE)
getVAF(res)
getVAF(res, part="common")
getVAF(res, part="distinctive", block="expr")