plot.confband.lines {sma}R Documentation

Adding Lines Satisfying a Confidence Criterion to the Current M vs A Plot

Description

This function adds 2 lines outlining the pointwise (intensity dependent) confidence band on the M vs A plot. The lines are drawn such that a prespecified proportion of points are outside the 2 confidence curves. The type of line may be specified as well as other parameters.

Usage

plot.confband.lines(x, M, crit1=0.025, crit2=crit1, nclass=10, ...)

Arguments

x a vector giving the x-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of average log intensities, ie A
M a vector giving the y-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of log intensity ratios.
crit1 The proportion of points less than the lower confidence curve. This takes a decimal value between 0 and 1.
crit2 The proportion of points greater than the upper confidence curve. By default, this has the same value as "crit1".
nclass A single number giving the approximate number of intensity depedent groups to consider.
... graphical parameters may also be supplied as arguments to the function (see par).

Value

Lines are added to the current plot.

Note

An M vs A plot must be constructed prior to the execution of this function.

See Also

plot.mva, stat.ma, lines, matlines, plot.confband.text, plot.confband.points .

Examples

data(MouseArray)
## mouse.setup <- init.grid
## mouse.data <- init.data

## To display an M vs A plot of the data 
plot.mva(mouse.data, mouse.setup) 

## Calculate M and A values 
mouse.lratio <- stat.ma(mouse.data, mouse.setup)

## To add default upper and lower confidence curves line to the M vs A plot
plot.confband.lines(mouse.lratio$A, mouse.lratio$M) 

[Package sma version 0.5.15 Index]