predictWrapper: A function returning predicted values for use with the fia...

In mrbin: Metabolomics Data Analysis Functions

A function returning predicted values for use with the fia function.

Description

This function predicts group membership and returns a numeric vector with results.

Usage

predictWrapper(
  model,
  dataSet,
  functionNamePredict = "predict",
  firstLevel = 1,
  parameterNameObject = "object",
  parameterNameData = "x",
  dataFrameFlag = FALSE,
  ...
)

Arguments

model	A predictive model. Make sure to have loaded all required packages before starting this function
dataSet	A matrix or dataframe containing data, depending on what your predict function requires. Columns=features, rows=samples
functionNamePredict	The name of the prediction function. This only needs to be changed if the prediction function is not called predict
firstLevel	Numeric value of first level or group. Usually 1 but for glm such as in the example this needs to be 0.
parameterNameObject	The name of the parameter for passing the model to the prediction function
parameterNameData	The name of the parameter for passing the data to the prediction function
dataFrameFlag	Logical value indicating whether the data object is a data frame rather than a matrix.
...	Optional, additional parameters that will be passed to the prediction function.

Value

A numeric (integer) vector of predicted group memberships.

Examples

 #First, define group membership and create the example feature data
 group<-factor(c(rep("Group1",4),rep("Group2",5)))
 names(group)<-paste("Sample",1:9,sep="")
 dataset<-data.frame(
   Feature1=c(5.1,5.0,6.0,2.9,4.8,4.6,4.9,3.8,5.1),
   Feature2=c(2.6,4.0,3.2,1.2,3.1,2.1,4.5,6.1,1.3),
   Feature3=c(3.1,6.1,5.8,5.1,3.8,6.1,3.4,4.0,4.4),
   Feature4=c(5.3,5.2,3.1,2.7,3.2,2.8,5.9,5.8,3.1),
   Feature5=c(3.2,4.4,4.8,4.9,6.0,3.6,6.1,3.9,3.5)
   )
 rownames(dataset)<-names(group)
 #train a model - here we use a logit model instead of ANN as a demonstration
 mod<-glm(group~Feature1+Feature2+Feature3+Feature4+Feature5,
   data=data.frame(group=group,dataset),family="binomial")
 predictWrapper(model=mod,dataSet=dataset,firstLevel=0,type="response")

mrbin documentation built on June 22, 2024, 9:39 a.m.