plsRcox (version 1.8.2)

coxsplsDR: Fitting a sPLSR model on the (Deviance) Residuals

Description

This function computes the Cox Model based on sPLSR components computed model with

• as the response: the Residuals of a Cox-Model fitted with no covariate

• as explanatory variables: Xplan.

It uses the package spls to perform the first step in SPLSR then mixOmics to perform PLSR step fit.

Usage

coxsplsDR(Xplan, ...)
# S3 method for default
coxsplsDR(
  Xplan,
  time,
  time2,
  event,
  type,
  origin,
  typeres = "deviance",
  collapse,
  weighted,
  scaleX = TRUE,
  scaleY = TRUE,
  ncomp = min(7, ncol(Xplan)),
  modepls = "regression",
  plot = FALSE,
  allres = FALSE,
  eta = 0.5,
  trace = FALSE,
  ...
)
# S3 method for formula
coxsplsDR(
  Xplan,
  time,
  time2,
  event,
  type,
  origin,
  typeres = "deviance",
  collapse,
  weighted,
  scaleX = TRUE,
  scaleY = TRUE,
  ncomp = min(7, ncol(Xplan)),
  modepls = "regression",
  plot = FALSE,
  allres = FALSE,
  dataXplan = NULL,
  subset,
  weights,
  model_frame = FALSE,
  eta = 0.5,
  trace = FALSE,
  model_matrix = FALSE,
  contrasts.arg = NULL,
  ...
)

Value

If allres=FALSE :

cox_splsDR

Final Cox-model.

If allres=TRUE :

tt_splsDR

sPLSR components.

cox_splsDR

Final Cox-model.

splsDR_mod

The sPLSR model.

Details

If allres=FALSE returns only the final Cox-model. If allres=TRUE returns a list with the sPLS components, the final Cox-model and the sPLSR model. allres=TRUE is useful for evluating model prediction accuracy on a test sample.

References

plsRcox, Cox-Models in a high dimensional setting in R, Frederic Bertrand, Philippe Bastien, Nicolas Meyer and Myriam Maumy-Bertrand (2014). Proceedings of User2014!, Los Angeles, page 152.

Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Philippe Bastien, Frederic Bertrand, Nicolas Meyer and Myriam Maumy-Bertrand (2015), Bioinformatics, 31(3):397-404, doi:10.1093/bioinformatics/btu660.

See Also

coxph, plsr

Examples

data(micro.censure)
data(Xmicro.censure_compl_imp)

X_train_micro <- apply((as.matrix(Xmicro.censure_compl_imp)),FUN="as.numeric",MARGIN=2)[1:80,]
X_train_micro_df <- data.frame(X_train_micro)
Y_train_micro <- micro.censure$survyear[1:80]
C_train_micro <- micro.censure$DC[1:80]

(cox_splsDR_fit=coxsplsDR(X_train_micro,Y_train_micro,C_train_micro,ncomp=6,eta=.5))
(cox_splsDR_fit2=coxsplsDR(~X_train_micro,Y_train_micro,C_train_micro,ncomp=6,eta=.5,trace=TRUE))
(cox_splsDR_fit3=coxsplsDR(~.,Y_train_micro,C_train_micro,ncomp=6,
dataXplan=X_train_micro_df,eta=.5))

rm(X_train_micro,Y_train_micro,C_train_micro,cox_splsDR_fit,cox_splsDR_fit2,cox_splsDR_fit3)