summary.qb.scanone {qtlbim}R Documentation

Summary of qb.scanone or qb.scantwo object.

Description

Summary of a qb.scanone or qb.scantwo object.

Usage

## S3 method for class 'qb.scanone':
summary(object, chr, threshold = 0,
  sort = "no", n.qtl = 0.05, ...)
## S3 method for class 'qb.scantwo':
summary(object, chr, threshold = 0,
  sort = "no", which.pos = "upper", min.iter,
  refine = FALSE, width = 10, smooth = 3, n.qtl = 0.05,
  weight = c("sqrt","count","none"), ...)
## S3 method for class 'summary.qb.scantwo':
print(x, digits = 3, ...)

Arguments

object A qb.scanone or qb.scantwo object.
x An object of class qb.scantwo.
chr Chromosomes to include in summary (must be integers for now).
threshold Threshold(s) for inclusion in summary (see below).
sort Sort by selected column of object ("no" indicates sort by chromosome).
which.pos Base position estimate on this summary for maximal statistics such as LOD.
min.iter Minimum number of iterations included at each position (default gleaned from object).
refine Refine estimates if TRUE.
width Window width for refinement.
smooth Degree of nearest neighbor smoothing to determine maxima.
n.qtl Minimum number of estimated QTL per chromosome or chromosome pair.
weight Weights to use for nearest neighbor smoothing. sqrt is square root of count per locus. Used only if smooth > 0.
digits Significant digits to round with print.
... Additional arguments for multiple linked loci (see details).

Details

These summary method report estimates by chromosome (or chromosome pair) at the maximum poster. Threshold can be used to condense summary to a subset of chromosomes (or chromosome pairs). Threshold is a vector with names corresponding to a subset of column names of object. Positive threshold values select chromosomes where that column average is above given value; negative threshold values select chromosomes with mean value within that value of the maximum across chromosomes. Thresholding is inclusive rather than exclusive.

It can be helpful to use summary.qb.scanone as an initial screen of chromosomes worth a further look. Since marginal summaries can include effects of multiple QTL and epistasis. Subsets based on 1-D scans can be used for 2-D subsequent screens. See qb.demo for an example.

Value

Matrix with chromosome chr, estimated position pos (or chromosome pairschr1 and chr2 and two columns for pos1 and pos2 in the case of summary.qb.scantwo) and means or modes of each column of object. Means are weighted by a smooth average of the number of MCMC sample iterations.

Author(s)

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

References

http://www.qtlbim.org

See Also

qb.scanone, plot.qb.scanone, qb.split.chr

Examples

data(qbExample)

temp <- qb.scanone(qbExample)
summary(temp, threshold = c(sum=15), sort = "sum")

temp <- qb.scantwo(qbExample)
summary(temp, threshold = c(upper=3), sort = "upper")

[Package qtlbim version 1.9.3 Index]