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, covar,
      adjust.covar, chr, sum.scan = "yes", min.iter = 1,
      aggregate = TRUE, 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` | 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`.
`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` 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

    ## 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 = "cellmean")
    summary(temp)
    plot(temp)

[Package qtlbim version 1.6.5 Index]