R: Plot 1-d LOD profiles for a multiple QTL model

plotLodProfile {qtl} | R Documentation

## Plot 1-d LOD profiles for a multiple QTL model

### Description

Use the results of `refineqtl` to plot one-dimensional LOD profiles for each QTL.

### Usage

    plotLodProfile(qtl, chr, incl.markers=TRUE, gap=25, lwd=2, lty=1, col="black",
                   qtl.labels=TRUE, mtick=c("line", "triangle"),
                   show.marker.names=FALSE, alternate.chrid=FALSE,
                   add=FALSE, showallchr=FALSE, labelsep=5, ...)

### Arguments

`qtl` | An object of class `"qtl"`; must have been produced by `refineqtl` using `keeplodprofiles=TRUE`.
`chr` | Optional vector indicating the chromosomes to plot. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`incl.markers` | Indicate whether to plot line segments at the marker locations.
`gap` | Gap separating chromosomes (in cM).
`lwd` | Line widths for each QTL trace (length 1 or the number of QTL).
`lty` | Line types for each QTL trace (length 1 or the number of QTL).
`col` | Line col for each QTL trace (length 1 or the number of QTL).
`qtl.labels` | If TRUE, place a label on each QTL trace.
`mtick` | Tick mark type for markers (line segments or upward-pointing triangels).
`show.marker.names` | If TRUE, show the marker names along the x axis.
`alternate.chrid` | If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.
`add` | If TRUE, add curves to a current plot.
`showallchr` | If FALSE (the default), only show the chr with a QTL
`labelsep` | If `qtl.labels=TRUE`, separation between peak LOD and QTL label, as percent of the height of the plot.
`...` | Passed to the function `plot` when it is called.

### Details

The function plots LOD profiles in the context of a multiple QTL model, using a scheme best described in Zeng et al. (2000). The position of each QTL is varied, keeping all other loci fixed. If a QTL is isolated on a chromosome, the entire chromosome is scanned; if there are additional linked QTL, the position of a QTL is scanned over the largest interval possible without allowing the order of QTLs along a chromosome to change. At each position for the QTL being scanned, we calculate a LOD score comparing the full model, with the QTL of interest at that particular position (and all others at their fixed positions) to the model with the QTL of interest (and any interactions that include that QTL) omitted.

Care should be take regarding the arguments `lwd`, `lty`, and `col`; if vectors are given, they should be in the order of the QTL within the object, which may be different than the order in which they are plotted. (The LOD profiles are sorted by chromosome and position.)

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### References

Zeng Z.-B., Liu, J., Stam, L. F., Kao, C.-H., Mercer, J. M. and Laurie, C. C. (2000) Genetic architecture of a morphological shape difference between two Drosophila species. Genetics 154, 299–310.

### See Also

`refineqtl`, `makeqtl`, `scanqtl`

### Examples

    data(fake.bc)

    fake.bc <- calc.genoprob(fake.bc, step=2)
    qtl <- makeqtl(fake.bc, chr=c(2,5), pos=c(32.5, 17.5), what="prob")

    out <- scanone(fake.bc, method="hk")

    # refine QTL positions and keep LOD profiles
    rqtl <- refineqtl(fake.bc, qtl=qtl, method="hk", keeplodprofile=TRUE)

    # plot the LOD profiles
    plotLodProfile(rqtl)

    # add the initial scan results, for comparison
    plot(out, add=TRUE, chr=c(2,5), col="red")

[Package qtl version 1.46-2 Index]