epsout.ld.snp {chopsticks} | R Documentation

## Function to write an eps file directly to visualize LD

### Description

`epsout.ld.snp` takes an object of `snp.matrix` class and a given snp range and depth, draw a eps file to visualize the LD in the same color scheme as haploview's default view. It was the first prototype of this bunch of software. Also, it does not keep any pair-wise data in memory at all, and maybe more suitable where the actual pair-wise LD data is not needed.

### Usage

    epsout.ld.snp(snpdata, filename, start, end, depth, do.notes=FALSE)

### Arguments

`snpdata` | An object of `snp.matrix` class with M samples of N snps
`filename` | The file name of the output, preferably ending with ".eps", but this rule not enforced
`start` | The index of the start of the range of interest. Should be between 1 and (N-1)
`end` | The index of the end of the range of interest. Should be between 2 and N.
`depth` | The depth or lag of pair-wise calculation. Should be between 1 and N-1
`do.notes` | Boolean for whether to generate pdf annotation-related code

### Details

The functinality of this routine has since been split into a two-stage processes involving `ld.snp` which generates a `snp.dprime` object which contains the result of the pairwise LD calculation, and `plot.snp.dprime` (or the `plot` method of a `snp.dprime` object) which does the drawing.

### Value

return nothing

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### References

Clayton, D.G. and Leung, Hin-Tak (2007) An R package for analysis of whole-genome association studies. Human Heredity 64:45-51.
GSL (GNU Scientific Library) http://www.gnu.org/software/gsl/
The postscript language reference manual: http://www.adobe.com/products/postscript/pdfs/PLRM.pdf
The pdf specification: http://partners.adobe.com/public/developer/en/pdf/PDFReference16.pdf

### See Also

`snp.dprime-class`, `ld.snp`, `plot.snp.dprime`

### Examples

    #
    data(testdata)
    epsout.ld.snp(Autosomes, start=1, end=500, depth=50, filename="test.eps")

[Package chopsticks version 1.48.0 Index]