R: SNP correlation plot

snpCorrelationPlot {GWASTools}

R Documentation

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

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)

[Package GWASTools version 1.24.1 Index]