R: function to plot GWAA results

plot.scan.gwaa {GenABEL} | R Documentation

## function to plot GWAA results

### Description

Plots results of GWA analysis

### Usage

    	## S3 method for class 'scan.gwaa'
    plot(x, y, ..., df=1, ystart=0, col=c("blue","green"),
    		sort=TRUE, ylim, delta = 1 , main = getcall(x))

### Arguments

`x` | object of type `scan.gwaa-class`, as returned by `scan.glm`, `qtscore`, `ccfast`, `emp.ccfast`, `emp.qtscore`, or `scan.haplo`
`y` | this argument is not used
`...` | additional arguments to be passed to plot
`df` | Plot results of 1 or 2-df test (1, 2). Could be also "Pc1df" (for GC corrected P-values) and "Pc2df" (for robust genomic control of the 2 df test)
`ystart` | truncate lower value of Y at this point (can help avoiding plotting too may points)
`ylim` | ylim, same as in the standard plot function
`col` | which colors to use to depict consecutive chromosomes
`sort` | whether results should be plotted after sorting by chromosome and position
`delta` | gap width between chromosomes
`main` | title of the plot

### Value

No value returned.

### Author(s)

Yurii Aulchenko

### See Also

`scan.gwaa-class`, `add.plot`, `snp.subset`, `scan.glm`, `qtscore`, `ccfast`, `emp.qtscore`, `emp.ccfast`, `scan.haplo`

### Examples

    require(GenABEL.data)
    data(srdta)
    a <- qtscore(bt,srdta,snps=c(1:250))
    plot(a)
    add.plot(a,df="Pc1df",col="green")

[Package GenABEL version 1.8-0 Index]