summary.qb.scanone {qtlbim} | R Documentation

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

### Description

Summary of a qb.scanone object.

### Usage

    ## S3 method for class 'qb.scanone':
    summary(object, chr, threshold = 0,
      sort = "no", smooth = 3, n.qtl = 0.05,
      min.iter, ...)
    ## 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, ...)

### Arguments

`object` | A `qb.scanone` object.
`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.
`...` | Not used.

### 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 `demo(qb.qb.scan.tour)` for an example.

### Value

Matrix with chromosome `chr`, estimated position `pos` (or chromosome pairs`chr1` 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 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`

### Examples

    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 1.6.5 Index]