plot.permTestResultsList: Function for plotting the results from a...

In bernatgel/regioneR: Association analysis of genomic regions based on permutation tests

Function for plotting the results from a permTestResultsList object when more than one evaluation function was used.

Description

Function for plotting the results from a permTestResultsList object when more than one evaluation function was used.

Usage

## S3 method for class 'permTestResultsList'
plot(
  x,
  ncol = NA,
  pvalthres = 0.05,
  plotType = "Tailed",
  main = "",
  xlab = NULL,
  ylab = "",
  ...
)

Arguments

x	an object of class permTestResultsList.
ncol	number of plots per row. ncol=NA means ncol=floor(sqrt(length(x)))so the plot is more or less square (default=NA)
pvalthres	p-value threshold for significance. Default is 0.05.
plotType	the type of plot to display. This must be one of "Area" or "Tailed". Default is "Area".
main	a character specifying the title of the plot. Defaults to "".
xlab	a character specifying the label of the x axis. Defaults to NULL, which produces a plot with the evaluation function name as the x axis label.
ylab	a character specifying the label of the y axis. Defaults to "".
...	further arguments to be passed to or from methods.

Value

A plot is created on the current graphics device.

See Also

permTest

Examples

genome <- filterChromosomes(getGenome("hg19"), keep.chr="chr1")
A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) 
B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))

pt <- overlapPermTest(A=A, B=B, ntimes=10, genome=genome, non.overlapping=FALSE)
summary(pt)
plot(pt)
plot(pt, plotType="Tailed")  
 
pt2 <- permTest(A=A, B=B, ntimes=10, alternative="auto", genome=genome, evaluate.function=list(distance=meanDistance, numberOfOverlaps=numOverlaps), randomize.function=randomizeRegions, non.overlapping=FALSE)
summary(pt2)
plot(pt2)
plot(pt2, plotType="Tailed")

bernatgel/regioneR documentation built on Sept. 10, 2023, 12:03 a.m.