subset: Subsetting Bayesian interval mapping data
In byandell/qtlbim: QTL Bayesian Interval Mapping

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

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

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

`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, logical 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` and `region` selection to linked loci all in selected subset.
`pheno.col`	Numeric or character identifier for phenotype. Useful eventually for multiple traits.
`...`	additional arguments to `subset`

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. Further subsets to only include QTL from these iterations that are on chromosomes chr.

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

http://www.qtlbim.org

read.cross

data(qbExample)

## 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)))