xyplot: Plot prediction regions and normalized intensities.

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot prediction regions for integer copy number and normalized intensities.

Usage

1

Arguments

x

A formula.

data

A CNSet object.

...

Additional arguments passed to xyplot function in lattice.

Value

A trellis object.

Author(s)

R. Scharpf

See Also

xyplot, ABpanel

Examples

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library(oligoClasses)
data(cnSetExample2)
table(batch(cnSetExample2))
sample.index <- which(batch(cnSetExample2) == "CUPID")
## A single SNP
pr <- predictionRegion(cnSetExample2[1:4, sample.index], copyNumber=0:4)
gt <- calls(cnSetExample2[1:4, sample.index])
lim <- c(6,13)
xyplot(B~A|snpid, data=cnSetExample2[1:4, sample.index],
       predictRegion=pr,
       panel=ABpanel,
       pch=21,
       fill=c("red", "blue", "green3")[gt],
       xlim=lim, ylim=lim)

## multiple SNPs, prediction regions for 3 batches
## Not run: 
	tab <- table(batch(cnSetExample2))
	bns <- names(tab)[tab > 50]
	sample.index <- which(batch(cnSetExample2) 
	pr <- predictionRegion(cnSetExample2[1:10, sample.index], copyNumber=0:4)
	gt <- as.integer(calls(cnSetExample2[1:10, sample.index]))
	xyplot(B~A|snpid, data=cnSetExample2[1:10, sample.index],
	       predictRegion=pr,
	       panel=ABpanel,
	       pch=21,
	       fill=c("red", "blue", "green3")[gt],
	       xlim=c(6,12), ylim=c(6,12))

	## nonpolymorphic markers
	data(cnSetExample2)
	tab <- table(batch(cnSetExample2))
	bns <- names(tab)[tab > 50]
	sample.index <- which(batch(cnSetExample2)
	np.index <- which(!isSnp(cnSetExample2))[1:10]
	taus <- tau2(cnSetExample)[np.index, , , ]
	pr <- predictionRegion(cnSetExample2[np.index, sample.index],
			       copyNumber=0:4)
	pp <- posteriorProbability(cnSetExample2[np.index, sample.index],
				   predictRegion=pr,
				   copyNumber=0:4)

## End(Not run)

benilton/crlmm documentation built on Dec. 27, 2019, 12:12 a.m.