snpCorrelationPlot: SNP correlation plot
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Author(s) See Also Examples

Plots SNP correlation versus chromosome.

1 2	snpCorrelationPlot(correlations, chromosome, ylim=c(0,1), ylab = "abs(correlation)", ...)

`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`.

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.

Cathy Laurie

manhattanPlot

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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)

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