qqPlot {GWASTools} | R Documentation

## QQ plot for genome wide assocation studies

### Description

Generates a Quantile-Quantile plot for -log10 p-values from genome wide association tests.

### Usage

    qqPlot(pval, truncate = FALSE, ylim = NULL, thinThreshold = NULL, ci=TRUE, ...)

### Arguments

`pval` | Vector of p-values
`truncate` | Either a logical value indicating whether the y-axis should be truncted to the same range as the x-axis, or a numeric value indicating where to truncate the y-axis. See details.
`ylim` | Limits for the y axis. Ignored if `truncate=TRUE` or `truncate` is numeric.
`thinThreshold` | if not `NULL`, `-log10(pval)` threshold for thinning points.
`ci` | logical indicator for whether to add confidence intervals to plots?
`...` | Other parameters to be passed directly to `plot`.

### Details

The function generates a Quantile-Quantile plot of p-values on a -log10 scale, with the option of truncating the y-axis to the range of the x-axis `(0, -log10(1/length(pval))`. If the y-axis is truncated, then points off the top of the plot are denoted by triangles at the upper edge. The 95% confidence interval is shaded in gray.

If truncate is set to a numeric value, then `ylim` is set to `c(0, truncate)` only if the value of truncate is bigger than the maximum `-log10(pval)`. (Use the `ylim` argument if alternatve behavior is desired.)

If requested with `thinThreshold`, points with p-values `< -log10(thinThreshold)` are thinned before plotting. All points with `-log10(pval) >= thinThreshold` plus 10,000 points with `-log10(pval) < thinThreshold` (randomly selected in uniformly-spaced bins of -log10(pval)) are displayed.

### Author(s)

Cathy Laurie, Matthew P. Conomos, Adrienne Stilp

### Examples

    pvals <- seq(0, 1, 0.001)
    qqPlot(pvals)
    qqPlot(pvals, thinThreshold=2)
    qqPlot(pvals, truncate=TRUE)
    qqPlot(pvals, truncate=10)

[Package GWASTools version 1.40.0 Index]