add.sig.thr {DOQTL} | R Documentation

## 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)

[Package DOQTL version 1.16.2 Index]