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]