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, pheno.col, ...)

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, 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

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. 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

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)))

[Package qtlbim version 1.9.3 Index]