subset.qb {qtlbim} | R Documentation |
Subset Bayesian interval mapping iterations on number of QTL and/or chromosome pattern of QTL, using exact match or inclusive subsetting.
## 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
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)))