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

subset.qb(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.ssg.uab.edu/qtlbim

See Also

read.cross

Examples


## Subset to chr 1,3,5.
qbSubset <- subset(qbExample, chr = c(1,3,5))

## Subset to chr 1,3,5 but restrict to only pairs with 1,3,5.
qbSubset <- subset(qbExample, chr = c(1,3,5), restrict.pair = TRUE)

## Subset to chr 1,3,5, and to within 10 cM of QTL on chr 3,5.
qbSubset <- subset(qbExample, chr = c(1,3,5),
  region = data.frame(chr = c(3,5), start = c(2,5), end = c(22,25)))

[Package qtlbim version 1.6.0 Index]