SPreFuGED (version 1.0)

estimateDataCha: A function to estimate data characteristics

Description

This function fits limma models (or univariate Cox's models t) to determine DE (informative) genes and then computes the proportion of DE (informative) genes, log2FC (coefficients or betas), pairwise correlation of DE (informative) and noisy genes, genes' variances, sample sizes and proportion of events (for survival data).

Usage

estimateDataCha(data, dataY, type = "Binary")

Arguments

data

a matrix of expression values with rows corresponding to genes and columns to samples

dataY

a binary vector of class labels or a survival outcome as produced by Surv. Its length must be equal to the number of columns of data.

type

takes Binary(Default) or Survival as values and correspond to binary classification or survival prediction

Value

A 1x7 (for Binary) or 1x8 (for Survival) matrix containing the estimates (row) of the data characteristics (columns)

Details

At the moment, only binary classification has been implemented.

References

Jong VL, Novianti PW, Roes KCB & Eijkemans MJC. Selecting a classification function for class prediction with gene expression data. Bioinformatics (2016) 32(12): 1814-1822

See Also

fitLMEModel, SPreFu and plotSPreFu

Examples

#Let us consider a single simulated train data as our real-life dataset
myCov<-covMat(pAll=100, lambda=2, corrDE=0.75, sigma=0.25);
myData<-generateGED(covAll=myCov, nTrain=30, nTest=10);
data<-myData[[1]]$trainData;
dataY<-myData[[1]]$trainLabels;
myDataCha<-estimateDataCha(data, dataY);