epsout.ld.snp: Function to write an eps file directly to visualize LD

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

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 [e-mail]

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")

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.