plot.qb.scantwo {qtlbim}R Documentation

Two dimensional LOD Plot of Epistasis/joint

Description

Plots joint LOD for chromosomes on a two dimensional grid.

Usage

print.qb.scantwo(x, ...)
plot.qb.scantwo(x, chr, smooth = 0, main, offset,
  lower = "joint", nodiag, slice = NULL,
  show.locus = TRUE, verbose = FALSE, ...)

Arguments

x An object of class qb.scantwo.
chr Vector of chromosomes to plot. Must be integer.
smooth Perform smoothing of smooth nearest neighbors.
main Main title.
offset Offset to make all values non-negative (see below).
lower This parameter is passed on to the plot.scanone function.
nodiag If TRUE do not include diagonal in plot.
slice Take 1-D slice through 2-D surface is not NULL (see below).
show.locus If a slice, show locus estimate if TRUE.
verbose Give verbose feedback if TRUE.
... Other parameters passed to generic plot function.

Details

The offset is used only if \line{qb.scantwo} used type = "estimate" to make values for plotting all non-negative. Values are rescaled by offset so that the origin is at 1 and, by default, the min and max are at 0 and 2, respectively, for each half of the plot. We need this at this time because plot.scantwo does not allow negative values.

The plot.scantwo arguments lower and nodiag are set to ensure values are all shown and not modified by plot.scantwo. The user is free to change them, but the plots may be non-sensical. For instance, change to lower = "cond-int" produces much white area on the image.

A non-null slice yields a 1-D view of the 2-D surface. The plots for slices use plot.scantwo. The elements of the slice vector are:

chr
Chromosome number to slice on.
upper
Focus on upper triangle of 2-D if TRUE.
start
Start position in chromosome chr (default = 0).
end
End position in chromosome chr (default = end of chromosome).
weight
Type of weighted mean across chr by number of MCMC samples: 0 = unweigthed; 1 = uniform weighting; 2 = position-specific weighting (default).

Value

The scantwo object being plotted.

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

References

http://www.ssg.uab.edu/qtlbim

See Also

qb.scantwo, plot.scantwo

Examples

example(qb.scantwo)

[Package qtlbim version 1.6.0 Index]