getAutoKM.list: getAutoKM.list

Description

Run the function "getAutoKM" for a list of models. More information in "?getAutoKM".

Usage

getAutoKM.list(
  type = "LP",
  lst_models,
  comp = 1:2,
  top = NULL,
  ori_data = TRUE,
  BREAKTIME = NULL,
  n.breaks = 20,
  minProp = 0.2,
  only_sig = FALSE,
  alpha = 0.05,
  title = NULL,
  subtitle = NULL,
  verbose = FALSE
)

Value

A list of two elements per each model in the list: info_logrank_num: A list of two data.frames with the numerical variables categorize as qualitative and the cutpoint to divide the data into two groups. LST_PLOTS: A list with the Kaplan-Meier Plots.

Arguments

type: Character. Kaplan Meier for complete model linear predictor ("LP"), for PLS components ("COMP") or for original variables ("VAR") (default: LP).
lst_models: List of Coxmos models.
comp: Numeric vector. Vector of length two. Select which components to plot (default: c(1,2)).
top: Numeric. Show "top" first variables. If top = NULL, all variables are shown (default: 10).
ori_data: Logical. Compute the Kaplan-Meier plot with the raw-data or the normalize-data to compute the best cut-point for splitting the data into two groups. Only used when type = "VAR" (default: TRUE).
BREAKTIME: Numeric. Size of time to split the data into "total_time / BREAKTIME + 1" points. If BREAKTIME = NULL, "n.breaks" is used (default: NULL).
n.breaks: Numeric. If BREAKTIME is NULL, "n.breaks" is the number of time-break points to compute (default: 20).
minProp: Numeric. Minimum proportion rate (0-1) for the group of lesser observation when computing an optimal cutoff for numerical variables (default: 0.2).
only_sig: Logical. If "only_sig" = TRUE, then only significant log-rank test variables are returned (default: FALSE).
alpha: Numeric. Numerical values are regarded as significant if they fall below the threshold (default: 0.05).
title: Character. Kaplan-Meier plot title. If NULL, Coxmos model name will be used (default: NULL).
subtitle: Character. Kaplan-Meier plot subtitle (default: NULL).
verbose: Logical. If verbose = TRUE, extra messages could be displayed (default: FALSE).

Author

Pedro Salguero Garcia. Maintainer: pedsalga@upv.edu.es

References

Kaplan_1958Coxmos

Examples

Run this code

data("X_proteomic")
data("Y_proteomic")

X_proteomic <- X_proteomic[1:30,1:20]
Y_proteomic <- Y_proteomic[1:30,]
set.seed(123)
index_train <- caret::createDataPartition(Y_proteomic$event, p = .5, list = FALSE, times = 1)
X_train <- X_proteomic[index_train,]
Y_train <- Y_proteomic[index_train,]
X_test <- X_proteomic[-index_train,]
Y_test <- Y_proteomic[-index_train,]
splsicox.model <- splsicox(X_train, Y_train, n.comp = 1, penalty = 0.5, x.center = TRUE,
x.scale = TRUE)
splsdrcox.model <- splsdrcox_penalty(X_train, Y_train, n.comp = 1, penalty = 0.5, x.center = TRUE,
x.scale = TRUE)
lst_models = list("sPLSICOX" = splsicox.model, "sPLSDRCOX" = splsdrcox.model)
getAutoKM.list(type = "LP", lst_models)

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