cvle-class {MicrobiomeSurv}

The cvle Class.

Description

Class of object returned by function CVLasoelascox.

Usage

## S4 method for signature 'cvle'
show(object)

## S4 method for signature 'cvle'
summary(object)

## S4 method for signature 'cvle,missing'
plot(x, y, type = 1, ...)

Arguments

object

A cvle class object

x

A cvle class object

y

missing

type

Plot type. 1 distribution of the HR under training and test set. 2 HR vs number selected taxa.

...

The usual extra arguments to generic functions — see plot, plot.default

Slots

Coef.mat

A matrix of coefficients with rows equals to number of cross validations and columns equals to number of taxa,

lambda

A vector of estimated optimum lambda for each iterations.

n

A vector of the number of selected taxa.

mi.mat

A matrix with 0 and 1. Number of rows equals to number of iterations and number of columns equals to number of taxa. 1 indicates that the particular taxon was selected or had nonzero coefficient and otherwise it is zero.

HRTrain

A matrix of survival information for the training dataset. It has three columns representing the estimated HR, the 95% lower confidence interval and the 95% upper confidence interval.

HRTest

A matrix of survival information for the test dataset. It has three columns representing the estimated HR, the 95% lower confidence interval and the 95% upper confidence interval.

pld

A vector of partial likelihood deviance at each cross validations.

Micro.mat

The microbiome matrix that was used for the analysis which can either be the full the full data or a reduced supervised PCA version.

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

EstimateHR, glmnet, Lasoelascox