summary.scanone: Summary of qb.scanone or qb.scantwo object.
In byandell/qtlbim: QTL Bayesian Interval Mapping

Description Usage Arguments Details Value Author(s) References See Also Examples

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

## 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","atten","ratten"), ...)
## S3 method for class 'summary.qb.scantwo'
print(x, digits = 3, ...)

`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. `atten` and `ratten` are attenuation based on `(1-2r)`. Used only if `smooth` > 0.
`digits`	Significant digits to round with print.
`...`	Additional arguments for multiple linked loci (see 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.

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.

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

http://www.qtlbim.org

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

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")