snpCorrelationPlot: SNP correlation plot

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

SNP correlation plot

Description

Plots SNP correlation versus chromosome.

Usage

snpCorrelationPlot(correlations, chromosome, 
                   ylim=c(0,1), ylab = "abs(correlation)", ...)

Arguments

correlations	A vector of correlations.
chromosome	A vector containing the chromosome for each SNP.
ylim	The limits of the y axis.
ylab	The label for the y axis.
...	Other parameters to be passed directly to plot.

Details

Plots SNP correlations (from, e.g., PCA), versus chromosome.

correlations must have the same length as chromosome and is assumed to be in order of position on each chromosome. Values within each chromosome are evenly spaced along the X axis.

Author(s)

Cathy Laurie

See Also

manhattanPlot

Examples

correlations <- sample(0.001*(0:1000), 1000, replace=TRUE)
chromosome <- c(rep(1,400), rep(2,350), rep("X",200), rep("Y",50))
snpCorrelationPlot(correlations, chromosome)

smgogarten/GWASTools documentation built on Nov. 10, 2024, 9:54 p.m.