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]