qqplotFast: Fast QQ-plot for Large Number of P-values
In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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

Function qqPlotFast creates a QQ-plot with a confidence band and an estimate of inflation factor lambda. It optimized to work quickly even for tens of millions of p-values.

qqPlotPrepare(
        pvalues,
        ntests = NULL,
        ismlog10 = FALSE)
qqPlotFast(
        x, 
        ntests = NULL, 
        ismlog10 = FALSE, 
        ci.level = 0.05, 
        ylim = NULL, 
        newplot = TRUE, 
        col = "#D94D4C", 
        cex = 0.5, 
        yaxmax = NULL, 
        lwd = 3, 
        axistep = 2, 
        col.band = "#ECA538",
        makelegend = TRUE,
        xlab = expression(
            paste("\u2013", " log"[10]*"(", italic("P"), "), null")),
        ylab = expression(
            paste("\u2013", " log"[10]*"(", italic("P"), "), observed")))

`pvalues`	Vector of p-values. As is (if `ismlog10 = FALSE`) or minus log10 transformed (if `ismlog10 = TRUE`).
`ntests`	If only significant p-values are provided, the total number of tests performed. By default `ntests` is equal to the length of `pvalues`.
`ismlog10`	Specifies whether the provides p-values (`pvalues` parameter) are minus log10 transformed (`- log10(pv)`)
`x`	Either a vector of p-values, as in `qqPlotPrepare`, or the object returned by `qqPlotPrepare`.
`ci.level`	Significance level of the confidence band. Set to `NULL` avoid plotting the confidence band.
`ylim`	Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters.
`newplot`	If `TRUE`, the function creates a new plot window.
`col`	The QQ-plot curve color.
`col.band`	Confidence band curve color.
`cex`	The size of QQ-plot points. As in Graphics Parameters.
`lwd`	The line width. As in Graphics Parameters.
`axistep`	Distance between axis label ticks for both axis.
`yaxmax`	Maximum reach of the y axis.
`makelegend`	If true, add legend to the plot.
`xlab, ylab`	Axis labels. As in plot function.

The function qqPlotFast creates a QQ-plot.
The function qqPlotPrepare extracts the necessary information from a vector of p-values sufficient for creating QQ-plot.
The resulting object is many times smaller than the vector of p-values.

The function qqPlotPrepare returns an object with the necessary information from a vector of p-values sufficient for creating QQ-plot.

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

The function works faster if the p-values are sorted.

Andrey A Shabalin andrey.shabalin@gmail.com

See vignettes: browseVignettes("ramwas").

# Million p-values
n = 1e6

# Null p-values
pv = runif(n)

# QQ-plot should be nearly diagonal
qqPlotFast(pv)
title("QQ-plot")

# Size of p-values before extraction of QQ-plot info
object.size(pv)

# Extract the QQ-plot info
qq = qqPlotPrepare(pv)

# Size of the QQ-plot info object
object.size(qq)

# Create QQ-plot, it is the same
qqPlotFast(qq)

# Create QQ-plot with plotting parameters
qqPlotFast(qq, ylim = c(0,10), yaxmax = 9, axistep = 3, lwd = 3, cex = 1)