pullSigQTL: Method to summarize scanone results

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

Description

pullSigQTL Uses qtlpvl to summarize the output of scanone, then culls the output to only significant QTL peaks, based on permutations.

Usage

pullSigQTL(cross, s1.output, perm.output, pheno.col = NULL, chr = NULL,
  alpha = 0.05, returnQTLModel = TRUE, ...)

Arguments

cross	The qtl cross.
s1.output	The output from scanone
perm.output	The permutation output from scanone
pheno.col	Character or numeric vector indicating the phenotype to be tested.
chr	The chromosome to be tested. Defaults to all chromosomes.
alpha	The significance for permutations
returnQTLModel	Logical, should a QTL model be returned (TRUE), or should a culled output from qtlpvl::convert_scan1 be returned (FALSE)?
...	additional arguments passed on to summary.scanone, such as controlAcrossCol.

Value

Either QTL models or simplified and converted scanone summary.

Examples

## Not run: 
library(qtlTools)
data(fake.bc)
cross<-fake.bc
cross <- calc.genoprob(cross, step=2.5)
s1<-scanone(cross, method="hk", pheno.col=c("pheno1", "pheno2"))
perm<-scanone(cross, n.perm=100, method="hk",
   pheno.col=c("pheno1", "pheno2"), verbose=FALSE)
pullSigQTL(cross, s1.output=s1, perm.output=perm)
pullSigQTL(cross, s1.output=s1, perm.output=perm, returnQTLModel=FALSE)

## End(Not run)

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