manhattan: Fast Manhattan plot for Large Number of P-values
In ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Description Usage Arguments Details Value Note Author(s) See Also Examples

The function manPlotFast creates a Manhattan plot.
The function manPlotPrepare extracts necessary information from a vector of p-values sufficient for creating a Manhattan plot.
It optimized to work quickly even for tens of millions of p-values.

manPlotPrepare(
        pvalues,
        chr,
        pos,
        ismlog10 = FALSE,
        chrmargins = 5e6)

manPlotFast(
        man,
        ylim = NULL,
        colorSet = c('steelblue4',"#2C82D1","#4CB2D1"),
        yaxmax = NULL,
        lwd = 3,
        axistep = 2,
        cex = 1)

`pvalues`	Vector of p-values. As is (if `ismlog10 = FALSE`) or minus log10 transformed (if `ismlog10 = TRUE`).
`chr, pos`	Vectors indicating the chromosomes and genomic positions (in basepairs) for each p-value in `pvalues`.
`ismlog10`	Specifies whether the provides p-values (`pvalues` parameter) are minus log10 transformed (`- log10(pv)`)
`chrmargins`	The plot margins at the ends of chromosomes (in basepairs).
`man`	Object returned by `manPlotPrepare`.
`ylim`	Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters.
`colorSet`	Colors of points, rotating over chromosomes. Points for first chromosome have color `colorSet[1]`, next `colorSet[2]`, etc. Once the colors are exhausted, the colors are reused from the beginning.
`yaxmax`	Maximum reach of the y axis.
`lwd`	The line width. As in Graphics Parameters.
`axistep`	Distance between axis label ticks for y axis.
`cex`	The size of Manhattan plot points. As in Graphics Parameters.

The function manPlotFast creates Manhattan plot.
It requires the use of the function manPlotPrepare which extracts the necessary information from a vector of p-values sufficient for creating Manhattan plot.
The resulting object is many times smaller than the vector of p-values.

This function manPlotPrepare returns an object with information for creating Manhattan plot.

The plot has no title. To add a title use title.

Andrey A Shabalin andrey.shabalin@gmail.com

See vignettes: browseVignettes("ramwas").

# Simulate data (9 chromosomes, million tests each)
chr = rep(paste0('chr',1:9), each = 1e6)
pos = rep(1:1e6, 9)
pv = runif(9e6)^1.1

# Extract the Manhattan plot info
man = manPlotPrepare(pv, chr, pos, chrmargins = 1000)

# Create Manhattan plot
manPlotFast(man)
title("Manhattan plot")

# Size of p-values before extraction of Manhattan plot info
object.size(list(pv, chr, pos))

# Size of the Manhattan plot info object
object.size(man)