qqnormGenomeWide {casper} | R Documentation

## Genome-wide qq-normal and qq-gamma plots

### Description

qqnormGenomeWide overlays quantile-quantile normal plots (qqnorm) for a series of genes (rows in the input matrix), to provide an overall assessment of Normality. Similarly, qqgammaGenomeWide overlays quantile-quantile gamma plots.

Note that the theoretical quantiles for z-scores under a Normal are the same for all genes, but the gamma theoretical quantiles depend on the Gamma parameter estimates for each gene and hence the theoretical quantiles are different for each gene (resulting in different x-values in each qq-plot)

### Usage

    qqnormGenomeWide(x, ngenes=min(1000, nrow(x)), ...)

    qqgammaGenomeWide(x, ngenes=min(1000, nrow(x)), ...)

### Arguments

`x` | `ExpressionSet`, `matrix` or `data.frame` with genes/isoforms in rows
`ngenes` | A qqnorm plot is produced for the first `ngenes` rows in `x`
`...` | Other arguments to be passed on to codeplot

### Value

Produces a figure overlaying qq-normal or qq-gamma plots for `ngenes` comparing observed vs. theoretical quantiles

### Author(s)

David Rossell

### Examples

    mu <- rnorm(100)
    x <- matrix(rnorm(100*5,mu),ncol=5)

    qqnormGenomeWide(x)
    qqgammaGenomeWide(exp(x))

[Package casper version 2.24.2 Index]