plot.scan.gwaa: function to plot GWAA results

In GenABEL: genome-wide SNP association analysis

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")

Example output

Loading required package: MASS
Loading required package: GenABEL.data
Warning messages:
1: In test.type(y, trait.type) : binomial trait is analysed as gaussian
2: In qtscore(bt, srdta, snps = c(1:250)) :
  11 observations deleted due to missingness
3: In qtscore(bt, srdta, snps = c(1:250)) : Lambda estimated < 1, set to 1

GenABEL documentation built on May 30, 2017, 3:36 a.m.