R: Indicate marker covariates from composite interval mapping

add.cim.covar {qtl} | R Documentation

## Indicate marker covariates from composite interval mapping

### Description

Add dots at the locations of the selected marker covariates, for a plot of composite interval mapping results.

### Usage

    add.cim.covar(cimresult, chr, gap=25, ...)

### Arguments

`cimresult` | Composite interval mapping results, as output from `cim`.
`chr` | Optional vector specifying which chromosomes to plot. (The chromosomes must be specified by name.) This should be identical to that used in the call to `plot.scanone`.
`gap` | Gap separating chromosomes (in cM). This should be identical to that used in the call to `plot.scanone`.
`...` | Additional plot arguments, passed to the function `points`.

### Details

One must first have used the function `plot.scanone` to plot the composite interval mapping results.

The arguments `chr` and `gap` must be identical to the values used in the call to `plot.scanone`.

Dots indicating the locations of the selected marker covariates are displayed on the x-axis. (By default, solid red circles are plotted; this may be modified by specifying the graphics parameters `pch` and `col`.)

### Value

A data frame indicating the marker covariates that were plotted.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`cim`, `plot.scanone`

### Examples

    ## Not run: data(hyper)
    hyper <- calc.genoprob(hyper, step=2.5)

    out <- scanone(hyper)
    out.cim <- cim(hyper, n.marcovar=3)
    plot(out, out.cim, chr=c(1,4,6,15), col=c("blue", "red"))

    add.cim.covar(out.cim, chr=c(1,4,6,15))
    ## End(Not run)

[Package qtl version 1.41-6 Index]