qb.arch {qtlbim} | R Documentation |
These routines work in conjunction with qb.hpdone
,
qb.scantwo
, qb.sliceone
and
step.fitqtl
to infer the number, pattern and position of
QTL from MCMC samples.
qb.arch(object, ...) ## Default S3 method: qb.arch(object, chr, pos, tolerance = 10, ...) ## S3 method for class 'step.fitqtl': qb.arch(object, main, epistasis, ...) ## S3 method for class 'qb.BestPattern': qb.arch(object, ...) ## S3 method for class 'qb.arch': summary(object, ...) ## S3 method for class 'qb.arch': print(x, ...)
object |
Object for appropriate method: summary of object of
class qb.scantwo for default; object of class
step.fitqtl . |
x |
Object of class qb.arch . |
chr |
Vector of chromosome numbers. |
pos |
Vector of positions on chromosomes (much be same length as chr ). |
tolerance |
Minimum distance for two QTL to be considered distinct. |
main |
Vector of chromosome identifiers with only main effects. |
epistasis |
Data frame with a 2-element vector of chromosome identifiers for each epistatic pair. |
... |
Not used here. |
Extract architecture in terms of chromosomes and positions of main QTL
and identifiers of epistatic pairs of QTL. The step.fitqtl
approach is used to compare an automatic fit to a user-defined set of
main chromosomes and epistatic pairs.
qtl |
Data frame with main QTL as chr and pos . |
by.num |
Data frame with epistatic pairs indexed by chromosome
number, labeled qtla and qtlb . |
by.chr |
List with elements chr and pos showing
epistatic pairs. These elements are data frames with chromosomes and
positions for each epistatic pair: rows are QTL number, columns are
qtla and qtlb . |
by.set |
List of connected sets of epistatic chromosomes. |
Brian S. Yandell
http://www.qtlbim.org
step.fitqtl
, qb.sweave
, qb.best
data(qbExample) ## Run qb.scantwo and get summary to use in qb.arch temp <- summary(qb.scantwo(qbExample, type = "2logBF"), threshold = c(upper = 10)) ## qb.arch default use. cross.arch <- qb.arch(temp, chr = c(1,1,2,3), pos = c(15,45,12,15)) cross.arch