qqnormGenomeWide: Genome-wide qq-normal and qq-gamma plots

In casper: Characterization of Alternative Splicing based on Paired-End Reads

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))

casper documentation built on Dec. 17, 2020, 2:01 a.m.