segmentsOnPeaks: Single QTL confidence intervals on LOD curves

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

segmentsOnPeaks Overlay confidence intervals onto a LOD plot, from as either plotLodProfile or plot.scanone.

Usage

segmentsOnPeaks(cross, calcCisOutput = NULL, ci.chr = NULL,
  peak = NULL, l = NULL, h = NULL, s1.output = NULL, mod = NULL,
  showallchr = FALSE, chr = NULL, pt.pch = 8, pt.cex = 0.8,
  pt.col = "red", int.y = 0, ...)

Arguments

cross	R/qtl cross object
calcCisOutput	The output from qtlTools::calcCis. If this is not supplied, ci.chr, peak, l, h must be. If calcCisOutput, these arguments are ignored
ci.chr	vector of chromosomes for segments
peak	vector of QTL peak positions (cM) for segments
l	vector of QTL lower confidence interval bounds (cM) for segments
h	vector of QTL upper confidence interval bounds (cM) for segments
s1.output	If plotting on a scanone LOD plot, provide the scanone object used previously.
mod	If plotting on lodProfile, pass the qtl model object that was input into plotLodProfile
showallchr	Must match call to plotLodProfile if qtl is specified
chr	If plotting on a specified set of chromosomes via scanone, replicate the chr call here.
pt.pch	pch parameter to points
pt.cex	cex parameter to points
pt.col	color parameter to points
int.y	the y intercept of the segments
...	additional parameters passed to segments, e.g. col, lty, etc.

Examples

## Not run: 
library(qtlTools)
data(fake.bc)
cross<-fake.bc
cross <- calc.genoprob(cross, step=2.5)

# Make a QTL object and formula
mod <- makeqtl(cross, chr = c(2,5), pos = c(40,25), what = "prob")
sex <- data.frame(sex = cross$phe$sex)
nform <- "y ~ Q1 + Q2 + Q1*sex + sex"
#Calculate lodprofiles for confidence interval estimation
mod <- refineqtl(cross, mod, pheno.col = "pheno1",
                 qtl = mod, formula = nform, covar = sex, method="hk")

cis<-calcCis(mod)
plotLodProfile(mod, showallchr=FALSE)
segmentsOnPeaks(cross, qtl = mod, calcCisOutput = cis,  showallchr=FALSE)

plotLodProfile(mod, showallchr=TRUE)
segmentsOnPeaks(cross, qtl = mod, calcCisOutput = cis, showallchr=TRUE)
cis<-calcCis(mod, drop = 3)
segmentsOnPeaks(cross, qtl = mod, calcCisOutput = cis, showallchr=TRUE,
   col = "purple", int.y=.5)

s1<-scanone(cross, method="hk", pheno.col="pheno1")
perm<-scanone(cross, n.perm=100, method="hk",pheno.col="pheno1", verbose=FALSE)
cis<-calcCis(s1.output=s1, perm.output=perm)
plot(s1)
segmentsOnPeaks(cross, s1.output=s1, calcCisOutput = cis)
plot(s1, chr = c(2,5))
segmentsOnPeaks(cross, s1.output=s1, calcCisOutput = cis, chr = c(2,5))

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.