Calculate pathway Confidence Intervals

Description

A function to calculate the confidence intervals for each of the gene sets in the geneResults object

Usage

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calcBayesCI(QSarray,low=0.025,up=1-low,addVIF=!is.null(QSarray$vif))
 

Arguments

QSarray

A QSarray object, as generated by either makeComparison or aggregateGeneSet

low, up

the lower and upper bounds of the confidence interval.

addVIF

a logical indicating whether the VIF should be used to calculate the variance of the pathway.

Details

This function can be used to calculate a confidence interval (CI) for the gene sets in QSarray. By default, a 95% CI is calculated, with the lower and upper bounds at 0.025% and 0.975%, respectively. This function is used in plotCIs to plot the confidence intervals of each pathway.

Value

Matrix of size (2 x numPathways(QSarray)) containing the lower and upper bounds of the confidence intervals for each pathway in QSarray.