qb.hpdone {qtlbim} | R Documentation |
Determine HPD region across genome, including position of posterior mode.
qb.hpdone(qbObject, level = 0.5, profile = "2logBF", effects = "cellmean", scan = "sum", chr, smooth = 3, ...) ## S3 method for class 'qb.hpdone': summary(object, chr, digits = 3, ...) ## S3 method for class 'qb.hpdone': print(x, ...) ## S3 method for class 'qb.hpdone': plot(x, chr, ...)
qbObject |
Object of class qb . |
object |
Object of class qb.hpdone . |
x |
Object of class qb.hpdone . |
level |
Value between 0 and 1 of HPD coverage. |
scan |
Elements to scan; usually one of "sum" ,
"mean" , "epistasis" , "GxE" . |
smooth |
Degree of smoothing. |
chr |
Chromosomes to include; default determined by HPD region. |
effects |
Effects are "cellmean" for means by genotype;
"estimate" for estimates of Cockerham main effects. |
profile |
Objective profile for plot; default is "2logBF" ;
other choices found in option type for
qb.scanone . |
digits |
Number of digits for round . |
... |
Extra parameters passed along to plot. |
Determine 100*level
percent HPD region. Subset chromosomes based
on HPD region. Create genome scans for profile
and effects
.
qb.hpdone
is a list with a hpd.region
summary matrix and
qb.scanone
objects for the profile
and
effects
. A summary of a qb.hpdone
object yields a matrix
with columns for
chr |
chromosome number |
n.qtl |
estimated number of QTL on chromosome |
pos |
estimated position of QTL |
lo.nn% |
lower nn% HPD limit |
hi.nn% |
upper nn% HPD limit |
profile |
Peak of profile, identifed by the profile type. |
effects |
Columns for the effects, appropriately labeled. |
Brian S. Yandell
http://www.qtlbim.org
data(qbExample) temp <- qb.hpdone(qbExample) summary(temp) plot(temp)