add.sig.thr: Add the significance thresholds to an existing QTL plot.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Add the significance thresholds to an existing QTL plot.

Description

Given a set of thresholds, add the autosomal and X chromosome thresholds to an existing QTL plot. The user may call plot() and then this function, but plot.doqtl contains a 'sig.thr' argument and will call this automatically. The threhsolds can be obtained from get.sig.thr

Usage

  add.sig.thr(sig.thr, sig.col = "red", chrsum)

Arguments

sig.thr	Numeric matrix or a numeric vector with the significance thredholds, typically obtained from get.sig.thr. If sig.thr is a matrix, then it must have 2 columns names 'A' and 'X' and each significance threshold is in one row.
sig.col	Numeric vector containing the plotting colors for each threshold. The length of sig.col must equal nrow(sig.thr).
chrsum	Numeric vector with the cumulative sum of the chromosome lengths. Must be named with chromosome names.

Value

Plots autosomal and X chromosome thresholds on a QTL plot. Behavior on other plots is undetermined.

Author(s)

Daniel Gatti

See Also

get.sig.thr

Examples

  ## Not run:  
     qtl = scanone(pheno = pheno, probs = probs, addcovar = addcovar, snps = anps)
     perms = scanone.perm(pheno = pheno, probs = probs, addcovar = addcovar, snps = anps)
     sig.thr = get.sig.thr(perms)
     plot(qtl)
     add.sig.thr(sig.thr, chrsum = cumsum(get.chr.lengths()))
     # Could also run:
     plot(qtl, sig.thr = sig.thr)
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.