qb.sliceone {qtlbim} | R Documentation |
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.
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)
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. |
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.
qb.sliceone
returns an object of class qb.sliceone
(a data frame) containing
effects selected according to type.scan
and scan
.
Brian S. Yandell, yandell@stat.wisc.edu
summary.qb.scanone
, plot.qb.scanone
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)