MultiplePLSCoxModels-class {plasma} | R Documentation |
Class "MultiplePLSCoxModels"
Description
The MultiplePLSCoxModels
object class ...
The validMultipleCoxModels
function checks if each data set contains the same set of samples.
The fitCoxModels
function fits many plsRcoxmodels and returns an S4 object of class MultiplePLSCoxModels
.
The getSizes
function returns a matrix with the list of dataframes of the MultiOmics
object as rownames and columns with NT, cNT, and p-values.
Usage
fitCoxModels(multi, timevar, eventvar, eventvalue, verbose)
## S4 method for signature 'MultiplePLSCoxModels'
summary(object, ...)
## S4 method for signature 'MultiplePLSCoxModels,missing'
plot(x, y, col = c("blue", "red"),
lwd = 2, xlab = "", ylab = "Fraction Surviving",
mark.time = TRUE, legloc = "topright", ...)
## S4 method for signature 'MultiplePLSCoxModels'
predict(object, newdata, type = c("components", "risk",
"split", "survfit"), ...)
Arguments
multi |
an object of class |
timevar |
a column in the |
eventvar |
a column in the |
eventvalue |
a character string specifying the value of the event in |
verbose |
logical; should the function report progress. |
object |
an object of class |
x |
an object of class |
y |
An ignored argrument for the plot method. |
col |
A vector of color specifications. Default is c(“blue”, “red”). |
lwd |
A vector specifying the line width. Default is “2”. |
xlab |
A character string to label the x-axis. Default is “”. |
ylab |
A character string to label the y-axis. Default is “Fraction Surviving”. |
mark.time |
A logical value; should tickmarks indicate censored data? Default is TRUE. |
legloc |
A character string indicating where to put the legend. Default is “topright”. |
... |
Other graphical parameters. |
newdata |
A |
type |
An enumerated character value. |
Value
The fitCoxModels
function retuns a newly constructed object of
the MultiplePLSCoxModels
class. The plot
method
invisibly returns the object on which it was invoked. The
summary
method returns no value. The predict method returns a
list of prediction results, each of which comes from the
predict
method for the SingleModel-class.
Slots
models
:A list of
SingleModel
objects, one for each assay.timevar
:A character matching the name of the column containing the time-to-event.
eventvar
:A character matching the name of the column containing the event.
eventvalue
:A character specifying the event in
eventvar.
Methods
plot
:Plots Kaplan-Meier curves for each omics dataset split into Low Risk and High Risk groups.
summary
:Returns a description of the
MultiplePLSCoxModels
object and the names of the omics datasets used to build the model.predict
:usually returns a list of numeric vectors of predicted risk per data type. When
type = "survfit"
, retuns a list ofsurvfit
objects.
Author(s)
Kevin R. Coombes krc@silicovore.com, Kyoko Yamaguchi kyoko.yamaguchi@osumc.edu
See Also
fitSingleModel
Examples
fls <- try(loadESCAdata())
if (inherits(fls, "try-error")) {
stop("Unable to load data from remote server.")
}
# restrict data set size
MO <- with(plasmaEnv, prepareMultiOmics(
assemble[c("ClinicalBin", "ClinicalCont", "RPPA")], Outcome))
splitVec <- with(plasmaEnv, rbinom(nrow(Outcome), 1, 0.6))
trainD <- MO[, splitVec == 1]
testD <- MO[, splitVec == 0]
firstPass <- fitCoxModels(trainD, "Days", "vital_status", "dead")
summary(firstPass)
plot(firstPass)
getSizes(firstPass)
pre1 <- predict(firstPass, testD)