calcBayesCI {qusage} | R Documentation

## Calculate pathway Confidence Intervals

### Description

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

### Usage

    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`.

[Package qusage version 2.21.0 Index]