IntegratedJM (version 1.6)

nullcov: nullcov

Description

The nullcov function is called while fitting the model when there no covariate is specified in the fitJM function. It returns a data.frame containing the results after fitting the model. The output of this function is also the output of the fitJM function.

Usage

nullcov(dat, responseVector, methodMultTest, data_type)

Arguments

dat

Contains the gene expression data matrix for all the genes - can be a matrix or an expression set.

responseVector

Vector containing the bio-activity data.

methodMultTest

Character string to specify the multiple testing method. Default is the BH-FDR method.

data_type

Binary, specifying the type of the parameter dat: 0 - expressionSet, 1 - matrix.

Value

A data frame, containing the results of the model - same as the output of the fitJM function.

Details

Fits the model using gls, calculates the correlation, p-values, adjusted p-values (based on the multiple testing method) and logratio from LRT and returns the required results.

Examples

# NOT RUN {
nullcov(dat=gene_eset,responseVector=activity,methodMultTest='fdr',data_type=0)
# }