subset.qb {qtlbim} | R Documentation

## Subsetting Bayesian interval mapping data

### Description

Subset Bayesian interval mapping iterations on number of QTL and/or chromosome pattern of QTL, using exact match or inclusive subsetting.

### Usage

    ## S3 method for class 'qb':
    subset(x, nqtl=1, pattern=NULL, exact=FALSE, chr,
      region, offset = TRUE, restrict.pair = TRUE, ...)

### Arguments

`x` | object of class `qb`
`nqtl` | subset on number of QTL
`pattern` | subset on chromosome pattern of QTL
`exact` | subset on exact pattern or number of QTL if true
`chr` | subset of chromosomes to plot (numerical indices or chromosome names)
`region` | list containing `chr`, and `start` and `end` positions, for regions to include
`offset` | indicates that `start` and `end` are in cM position if `TRUE`; otherwise they are in distance from first marker
`restrict.pair` | Restrict `chr` selection to epistatic pairs with both in selected subset.
`...` | additional arguments to `subset`

### Details

Subset to include only iterations with at least `nqtl` number of QTL and at least the `pattern` across chromosomes. `pattern` is a vector of chromosome identices, with repeats for multiple linked QTL on a chromosome. If `exact=FALSE`, then all iterations with at least the given `pattern` and `nqtl` are included. `nqtl` will be reset to `length(pattern)` if it is smaller than this value. Note that `pattern` should be number codes corresponding to those used in the `x` object. At present, chromosome names are not allowed. Further subsets to only include QTL from these iterations that are on chromosomes `chr`.

### Author(s)

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

### References

http://www.qtlbim.org

### See Also

`read.cross`

### Examples

    ## Subset to chr 1,2, and to within 10 cM of QTL on chr 1,2.
    qbSubset <- subset(qbExample, chr = c(1,2),
      region = data.frame(chr = c(1,2), start = c(35,2), end = c(55,22)))

[Package qtlbim version 1.6.5 Index]