non_nullcov {IntegratedJM}

non_nullcov

Description

The non_nullcov function is called while fitting the model when the 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

non_nullcov(dat, responseVector, covariate, 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.

covariate

Vector of 0's and 1's, containing data about the fingerprint feature.

methodMultTest

Character string to specify the multiple testing method.

data_type

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

Details

Fits the model, adjusting for the covariate effect, 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.

Value

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

Examples

## Not run: 
non_nullcov(dat=gene_eset,responseVector=activity,covariate=fp,methodMultTest='fdr',data_type=0)

## End(Not run)