cScale {geneplotter} | R Documentation

## A function for mapping chromosome length to a number of points.

### Description

Given a number of points (generally representing the number of points on a plot's axis), and a vector of chromosome lengths - will generate a vector of the same length as the one passed in containing scaling factors for each chromosome.

### Usage

    cScale(points, cLengths, method=c("max", "relative"), chrom)

### Arguments

`points` | The number of points to scale the chromosome length to.
`cLengths` | A vector of chromosome lengths.
`method` | Determines whether to use relative or absolute scaling. Default is "max" (absolute).
`chrom` | Which chrom to determine the scale for

### Details

The scale factor is calculated in a manner based on the `method` argument. If method is `max`, the factor is derived by dividing the points argument by each chromosome's length (in base pairs). If the method chosen is `relative`, then the scale is determined by dividing the points argument by the maximum chromsome length, and applying that value to each chromosome.

### Author(s)

Jeff Gentry

### See Also

`cPlot`

### Examples

       ## A bit of a hack to not have a package dependency on hgu95av2
       ## but need to fiddle w/ the warn level to not fail the example anyways.
       curWarn <- options(warn=0)
       on.exit(options(warn=curWarn), add=TRUE)
       if (require(hgu95av2)) {
          z <- buildChromLocation("hgu95av2")

         for (sc in c("max","relative"))
           scale <- cScale(1000, chromLengths(z),sc,"Y")
       } else print("This example needs the hgu95av2 data package")

[Package geneplotter version 1.12.0 Index]