plot.bayesian {sma}R Documentation

Plots lodscore vs effect estimate (the output of stat.bayesian() or stat.bay.est()).

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 ingrid@math.uu.se

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))


[Package sma version 0.5.15 Index]