manhattan: Manhattan plots for P-values
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Arguments Details Value Author(s) Examples

Plots a ‘Manhattan’ plot, appropriate for P-values from a genome-wide analysis.

1	manhattan(p, SNP, chr, pos, pmin = NULL, ...)

`p`	A vector of P-values
`SNP`	A vector of SNP names in chr:pos[:allele_allele] format
`chr`	A vector of chromosome locations
`pos`	A vector of positions within chromosomes
`pmin`	The smallest P-value that should fit in the plot
`...`	Additional arguments passed to points for plotting the p-values

The plot is drawn in the current screen on the current device. The spacing between chromosomes is hard coded to a value that looks nice for human chromosome lengths.

Nothing should be returned.

Toby Johnson Toby.x.Johnson@gsk.com

chr <- rep(c(1:22, "X"), each = 5000)
pos <- do.call(c, lapply(c(2e8/sqrt(1:22), 2e8),
                         function(chrlen)
                         return(sort(chrlen*runif(5000)))))
SNP <- paste(chr, pos, sep = ":")
pvals <- runif(115000)
manhattan(pvals, SNP, pch = 20)
## FIXME blue colour repeated for X