plot.bayesian: Plots lodscore vs effect estimate (the output of...

In gnyamundanda/sma: Statistical Microarray Analysis

Description

This function plots the results of stat.bayesian() or stat.bay.est() highlighting genes meeting userspecified criteria.

Usage

plot.bayesian(x=NULL, Mbar=x$Xprep$Mbar, lods=x$lods, 
type="t", spec=50, ch=NULL, col="black",...)

Arguments

x	output from stat.bayesian() or stat.bay.est()
Mbar	Effect estimate for each gene.
lods	Posterior lodsratio for each gene.
type	Type of criteria for highlighting genes (see details).
spec	Specifies cutoff etc. depending on type.
ch	Character with which to selected highlight genes. (Default is the gene index.)
col	Colour of highlighted genes. (Default is black.)
...	Additional graphical parameters

Details

If type='t', plot.bayesian() highlights the top spec genes. If type='c', plot.bayesian() highlights the genes with lods>=spec. If type='i', plot.bayesian() highlights the genes with indecies specified in spec.

Author(s)

Ingrid Lönnstedt [e-mail]

See Also

stat.bayesian,stat.bay.est

Examples

data(MouseArray)
## mouse.setup <- init.grid() 
## mouse.data <- init.data() ## see \emph{init.data} 
## mouse.lratio <- stat.ma(mouse.data, mouse.setup)
mouse.bayesian<-stat.bayesian(M=mouse.lratio$M)

plot.bayesian(mouse.bayesian)
plot.bayesian(mouse.bayesian,type='c',spec=0,col='blue')
plot.bayesian(mouse.bayesian,type='i',spec=c(1000,2000),col='green')
plot.bayesian(mouse.bayesian,type='i',spec=1:length(mouse.bayesian$lods))

gnyamundanda/sma documentation built on May 3, 2019, 5:17 p.m.