subset.bim {bim} | 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

subset.bim(x, cross, nqtl=1, pattern=NULL, exact=FALSE, chr, ... )

### Arguments

`x` |
object of class `bim` |

`cross` |
corresponding object of class `cross` |

`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) |

`...` |
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.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

### See Also

`read.bim`

### Examples

## Not run:
bim223 <- subset.bim( bim, pattern = c(2,2,3) )
## End(Not run)

[Package

*bim* version 1.01-1

Index]