qb.multloci {qtlbim} | R Documentation |
Summaries and up to four plots showing loci found in MCMC samples for a chromosome.
qb.multloci(qbObject, chr = 1, cutoff = 25, nqtl, ...) ## S3 method for class 'qb.multloci': plot(x, amount = 0.5, cex, split = TRUE, contour = TRUE, weight = TRUE, merge = TRUE, ...) ## S3 method for class 'qb.multloci': summary(object, merge = TRUE, ...)
qbObject |
Object of class qb . |
x,object |
Object of class qb.multloci . |
chr |
Identifier for one chromosome. |
cutoff |
Smallest posterior probability for nqtl (ignored
if nqtl provided). |
nqtl |
Number of QTL on chromosome (inferred by default). |
amount |
Amount to jitter points. |
cex |
Character expansion of plot symbols. |
split |
Split plots into four panels on one page if
TRUE . Otherwise plot each panel separately. The split
may be a numeric vector with values 1:4 signifying which panels to
show. See details. |
contour |
Contour plot overlaid on pairs if TRUE . |
weight |
Inversely weight loci in density plot by number of QTL
if TRUE . |
merge |
Merge across number of QTL if TRUE . Otherwise,
show separate summary or plot by number of QTL. See details. |
... |
Parameters to qb.mainmodes or to methods. |
Find multiple loci in MCMC samples for chromosome chr
. The
number of QTL, nqtl
is inferred from the histogram as the
largest number of QTL above the percent cutoff
.
The generic plot
command produces the following plots: (1)
density plot of main QTL grouped by QTL; (2) histogram of number of
QTL; (3) density plot of epistatic pairs; (4) scatter plot of pairs of
QTL. The density plots are divided into nqtl
groups. The
scatter plot shows pairs of main loci below diagonal and epistatic
pairs above using codes corresponding to the number of QTL per sample;
note that 3 QTL have 3 pairs, 4 QTL have 6, etc., and that solitary
QTL are displayed along the diagonal.
split
and merge
control the manner of plotting. Setting
merge
to FALSE
yields only density plots for main loci
conditioned on the number of QTL per sample. Setting split
to
FALSE
or to numbers between 1 and 4 yields plots on separate
pages.
Brian S. Yandell, yandell@stat.wisc.edu
plot.qb
, qb.scantwo
, qb.mainmodes
data(qbExample) temp <- qb.multloci(qbExample, 1) summary(temp) plot(temp) plot(temp, merge = FALSE) summary(temp, merge = FALSE)