plot.qb.mainmodes {qtlbim} | R Documentation |
Determine number of QTL per chromosome and estimate peaks and valleys.
qb.split.chr(qbObject, split, ...) qb.epimodes(qbObject, cutoff = 1, nqtl, n.iter, pairloci, ...) qb.mainmodes(qbObject, cutoff = 25, nqtl, n.iter, mainloci, ...) ## S3 method for class 'qb.mainmodes': summary(object, digits = 4, ...)
qbObject |
Object of class qb . |
split |
List of split locations; names of list must correspond to
chromosome names in qbObject . Default set by call to
qb.mainmodes with addition arguments in ... . |
object |
Object of class qb.mainmodes . |
cutoff |
Cutoff for neglible number of QTL. |
nqtl |
Vector of number of QTL per chromosome. |
n.iter |
Number of iterations (for internal use only). |
mainloci |
Object containing mainloci data (for internal
use only). |
pairloci |
Object containing pairloci data (for internal
use only). |
digits |
Number of significant digits. |
... |
Parameters to qb.mainmodes or to methods. |
Cut off histogram of number of QTL per chromosome such that cumulative
percent above number is less than cutoff
. Once nqtl
is
determined or provided in call, divide MCMC samples using linear
discriminant analysis (lda
) and find peak locations per
class. Use these peak locations to find locations of valleys between
peaks. These valleys are used to divide MCMC samples into separate QTL
for analysis. Currently this is used by summary.qb.scanone
and qb.multloci
.
qb.split.chr
sets up a split
for chromosomes
for at valleys between inferred multiple QTL as an
attribute of a returned qbObject
. This is done by default when
qbObject
is created, and is stored as an attribute available as
qb.get(qbObject, "split.chr")
.
Brian S. Yandell, yandell@stat.wisc.edu
qb.multloci
, summary.qb.scanone
data(qbExample) temp <- qb.mainmodes(qbExample) summary(temp)