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

In qtl: Tools for Analyzing QTL Experiments

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, [e-mail]

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")

qtl documentation built on Sept. 11, 2024, 5:43 p.m.