get_scores: Calculates principal scores for Poisson-noise corrected PCA

In PoissonPCA: Poisson-Noise Corrected PCA

Description

This function is based on principal component analysis of a transformation of latent Poisson means of a sample. Given the estimated principal components of the latent Poisson means, this function estimates scores using a combination of likelihood and mean squared error.

Usage

get_scores(X,V,d,k,transformation,mu)
get_scores_log(X,V,d,k,mu)

Arguments

X	The data matrix
V	Vector of all principal components of the transformed latent means
d	Eigenvalues corresponding to the principal components
k	Number of principal components to project onto
transformation	The transformation to be applied to the latent means
mu	The mean of the transformed latent means

Details

This function estimates the latent transformed Poisson means in order to minimise a combination of the log-likelihood plus the squared residuals of the projection of these latent means onto the first k principal components. Note that for transformed Poisson PCA, the scores are not nested, so the choice of k will have an impact on the projection. The get_scores_log function deals with the special case where the transformation is the log function.

Value

scores	The principal scores
means	The corresponding estimated latent Poisson means

Author(s)

Toby Kenney [e-mail] and Tianshu Huang

Examples

n<-20  #20 observations
p<-5   #5 dimensions
r<-2   #rank 2

mean<-10*c(1,3,2,1,1)

set.seed(12345)

Z<-rnorm(n*r)
dim(Z)<-c(n,r)
U<-rnorm(p*r)
dim(U)<-c(r,p)

Latent<-Z%*%U+rep(1,n)%*%t(mean)

X<-rpois(n*p,as.vector(Latent))
dim(X)<-c(n,p)

Sigma<-LinearCorrectedVariance(X[-n,])

eig<-eigen(Sigma)


get_scores(X[n,],eig$vectors,eig$values,r,"linear",colMeans(X[-n,]))

Xlog<-rpois(n*p,exp(as.vector(Latent)+3))
dim(Xlog)<-c(n,p)

logtrans<-makelogtransformation(3,4)

Sigmalog<-TransformedVarianceECV(X[-n,],logtrans$g,logtrans$ECVar)

eiglog<-eigen(Sigmalog)

gX<-X[-n,]

if(!is.null(logtrans)){
    for(i in 1:(n-1)){
        for(j in 1:p){
            gX[i,j]<-logtrans$g(X[i,j])
        }
    }
}                    

mu<-colMeans(gX)        


get_scores_log(X[n,],eiglog$vectors,eiglog$values,r,mu)

PoissonPCA documentation built on Aug. 17, 2021, 5:09 p.m.