qqPlot: QQ plot for genome wide assocation studies
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Author(s) Examples

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

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

`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`.

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.

Cathy Laurie, Matthew P. Conomos, Adrienne Stilp

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

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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