qb.sliceone {qtlbim}R Documentation

Genome Slice to detect QTL for Phenotypic Trait

Description

This method extracts iteration diagnostics and mainloci from the qb object and returns a data frame (of class qb.sliceone). Generic summary and plot can be used for display.

Usage

qb.sliceone(qbObject, slice, epistasis = TRUE, scan, type.scan, covar,
  adjust.covar, chr, sum.scan = "yes", min.iter = 1,
  aggregate = TRUE, smooth = 3, weight = c("sqrt","count","none"),
  split.chr, center.type = c("mode","mean","scan"), verbose = FALSE, ...)
## S3 method for class 'qb.sliceone':
summary(object, chr, ...)
## S3 method for class 'qb.sliceone':
print(x, ...)
## S3 method for class 'qb.sliceone':
plot(x, ..., scan, auto.par = TRUE)

Arguments

qbObject An object of class qb.
object Object of class qb.sliceone.
x Object of class qb.sliceone.
slice Chromosomes to slice upon.
epistasis If TRUE then information about epistasis is included.
scan Vector of diagnostics to scan (see below).
type.scan Type of scan; default is "heritability" (see below).
covar Covariate(s) to include; default is seq(nfixcov) where nfixcov is taken from qb.data. Set to 0 to exclude any covariates.
adjust.covar Adjustments to covariates. Default is NA, which adjusts by covariate mean values. Values are assumed to be in order of fixed covariates.
chr Chromosomes to subset on if not NULL.
sum.scan Sum over scan diagnostics if "yes" or "only"; only report sum if "only".
min.iter Include only samples at loci if minimum number of iterations is at least min.iter; default is to include all (min.iter = 1).
aggregate Aggregate effects into main, epis, gbye if TRUE.
smooth Degree of nearest neighbor smoothing to determine maxima.
weight Weights to use for nearest neighbor smoothing. sqrt is square root of count per locus. Used only if smooth > 0.
split.chr Split summary by multiple QTL per chromosome (see details for plot.qb.scanone).
center.type Method to find QTL loci. See details.
verbose Give verbose feedback if TRUE.
auto.par Automatic setting of plot parameters for multiple plots if TRUE.
... Arguments to be passed along.

Details

All arguments except slice agree with qb.scanone. The slice specifies a chromosome upon which to slice, yielding a 1-D scan of what might be seen on a 2-D scan using qb.scantwo. One advantage of qb.sliceone is that you can get 2-QTL cell means for the slice chromosome and the scanned chromosomes.

The summary invokes summary.qb.scanone to summarize slice by chromosome. The plot will by default give separate plots for each slice genotype and use plot.qb.scanone to scan the chromosomes. If scan is specified for plot.qb.sliceone, then those elements will be plotted. For instance, plot(x,scan="slice") will plot the running average locus on the slice chromosome with respect to the other chromosomes.

Value

qb.sliceone returns an object of class qb.sliceone (a data frame) containing effects selected according to type.scan and scan.

Author(s)

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

References

http://www.qtlbim.org

See Also

summary.qb.scanone, plot.qb.scanone

Examples

data(qbExample)

## Get profile of heritability.
temp <- qb.sliceone(qbExample, slice = 1, chr = 2:3)
summary(temp)
plot(temp)

## Get profile of cell means.
temp <- qb.sliceone(qbExample, slice = 1, chr = 2:3, type.scan = "cellmean")
summary(temp)
plot(temp)

[Package qtlbim version 1.9.3 Index]