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.

`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]