# scalecurve: Computation and Representation of the Scale Curve In depthTools: Depth Tools Package

## Description

`scalecurve` computes the scale curve of a given group, based on the modified band depth, at a given value p as the area of the band delimited by the [np] most central observations, where [np] is the largest integer smaller than np.

## Usage

 ```1 2``` ```scalecurve(x,y=NULL,xlab="p",ylab="A(p)",main="Scale curve",lwd=2, ...) ```

## Arguments

 `x` a data matrix containing the observations (samples) by rows and the variables (genes) by columns `y` an optional vector (numeric or factor) of length equal to the number of rows in `x`, containing the class of each observation. If unprovided, then all the elements in `x` are assumed to belong to a single class `xlab` label in the x axis `ylab` label in the y axis `main` plot title `lwd` line widths for the corresponding scale curve(s) `...` graphical parameters to be passed to 'plot'

## Details

The scale curve measures the increase in the area of the band determined by the fraction p most central curves, where p moves from 0 to 1, thus providing a measure of the sample dispersion. If the data set is represented in parallel coordinates, then the area is computed using the trapezoid formula.

## Value

 `r` the value of the scale curve at equidistant values of p, determined by the number of observation within each class. If `y` is not provided, then `r` is a vector, otherwise is a list with as many components as classes described by `y`.

## Author(s)

Aurora Torrente [email protected]

## References

Lopez-Pintado, S. et al. (2010). Robust depth-based tools for the analysis of gene expression data. Biostatistics, 11 (2), 254-264.

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23``` ```## scale curve of a single data set ## simulated data set.seed(0) x <- matrix(rnorm(100),10,10) scalecurve(x) ## real data data(prostate) prost.x<-prostate[,1:100] prost.y<-prostate[,101] scalecurve(prost.x[prost.y==0,]) ## scale curve of normal samples scalecurve(prost.x[prost.y==1,]) ## scale curve of tumoral samples ## scalecurve of different groups ## simulated data x <- matrix(rnorm(100),10,10) y <- c(rep("tumoral",5),rep("normal",5)) scalecurve(x,y) ## real data labels<-prost.y labels[prost.y==0]<-"normal"; labels[prost.y==1]<-"tumoral" scalecurve(prost.x,labels) ```

depthTools documentation built on May 30, 2017, 1:34 a.m.