MAPlot1 {aCGH.Spline}R Documentation

Produce a MAplot showing points retained vs. points excluded.

Description

Produce a MA-plot showing points retained and points excluded.

Usage

MAPlot1(x, pch=46, Retcol="black", Excol="red", ylim=c(-5,5), xlim=c(0,20), xlab="log2(mean(cy5, cy3))", ylab="log2(cy5/cy3)", main="MA-plot")

Arguments

x - ".temp" formatted data structure.
pch - the point character to use defaults to 46.
Retcol - the point color to use for the points retained after normalisation, defaults to "black".
Excol - the point color to use for the points excluded after normalisation, defaults to "red".
xlim - the x-axis limits defaults to c(0,20).
ylim - the y-axis limits defaults to c(-5,5).
xlab - the label for the x-axis.
ylab - the label for the y-axis.
main - the main title for the plot.

Value

Figure showing the log2(mean(red,green)) vs. the log2(red/green).

Author(s)

Tomas William Fitzgerald

Examples


## Set up noisy data with a bias
v = seq(1,100000,0.5)
d = sin(2*pi/500 * v) 
nd = d  +  rnorm(length(d),0,100) + 1000
dd = sin(2*pi/1000 * v) 
ndd = dd  +  rnorm(length(dd),0,120) + 1000
 
## Create ".temp" data stucture
mat = matrix(ncol=8,nrow=length(dd))
mat[,1] = log2(nd/ndd)
mat[,2] = nd
mat[,3] = ndd
mat[,4] = 0
mat[,5] = 0
mat[,6] = 0
mat[,7] = 0
mat[,8] = 0

## Add a few flags
mat[100:150,7] = 1

## Plot the data
par(mfrow=c(2,1),mar=c(1,1,1,1))
MAPlot1(mat,ylim=c(-1,1),xlim=c(9.4,10.4))


[Package aCGH.Spline version 2.2 Index]