lmdme-leverage: 'leverage' test of lmdme objects

In lmdme: Linear Model decomposition for Designed Multivariate Experiments

Description

This function calculates the leverage test for each individual using the Principal Component Analysis (comps function) on the coefficients of the given decomposed model term.

Arguments

object	lmdme class object.
comps	a numeric vector indicating the PCA component indexes to keep. Default the first two components (1:2).
term	a character specifying the model term.
level	the quantile level. Default value 0.95

Value

data.frame with the following fields

leverage	numeric for the corresponding row leverage
over	logical indicating if the leverage > quantile(leverage,level) for the given decomposed term

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

Tarazona S, Prado-Lopez S, Dopazo J, Ferrer A, Conesa A, Variable Selection for Multifactorial Genomic Data, Chemometrics and Intelligent Laboratory Systems, 110:113-122 (2012)

See Also

prcomp, quantile

Examples

{
data(stemHypoxia)

##Just to make a balanced dataset in the Fisher sense (2 samples per
## time*oxygen levels)
design<-design[design$time %in% c(0.5, 1, 5) & design$oxygen %in% c(1,5,21),]
design$time<-as.factor(design$time)
design$oxygen<-as.factor(design$oxygen)
rownames(M)<-M[, 1]

##Keeping appropriate samples only
M<-M[, colnames(M) %in% design$samplename]

##ANOVA decomposition
fit<-lmdme(model=~time+oxygen+time:oxygen, data=M, design=design)

##Leverages for the first two Principal Components and q95 (default value).
##Leverages for the first three Principal Components and q99.
leverages2PCDefault<-leverage(fit, term="time:oxygen")
leverages3PCq99<-leverage(fit, comps=1:3, term="time:oxygen", level=0.99)
}

Example output

Loading required package: pls

Attaching package: 'pls'

The following object is masked from 'package:stats':

    loadings

Loading required package: stemHypoxia

Attaching package: 'lmdme'

The following object is masked from 'package:stats':

    p.adjust

lmdme documentation built on Nov. 8, 2020, 7:46 p.m.