subset.bim {bim} | R Documentation |
Subset Bayesian interval mapping iterations on number of QTL and/or chromosome pattern of QTL, using exact match or inclusive subsetting.
subset.bim(x, cross, nqtl=1, pattern=NULL, exact=FALSE, chr, ... )
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 |
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
.
Brian S. Yandell, yandell@stat.wisc.edu
http://www.stat.wisc.edu/~yandell/qtl/software/bmqtl
## Not run: bim223 <- subset.bim( bim, pattern = c(2,2,3) ) ## End(Not run)