Description Usage Arguments Details Value Author(s) See Also Examples
Interactive graphical display of an IBD
object.
1 2 |
x |
an IBD object returned by IBDcheck |
kinshipth |
Kinship coefficient threshold.
If |
ellipse.coverage |
Prediction ellipse coverage probability.
Simulated pairs of subjects from
a given relationship are used to construct prediction ellipses with
approximate coverage probability |
... |
optional arguments passed to |
Overview:
When simulate=FALSE
, the function produces an interactive plot of
estimated IBD coefficients for pairs of study subjects whose estimated
kinship coefficients exceed the user-specified threshold in kinshipth
.
Plots are of the estimated probability of 1 IBD versus the estimated
probability of 0 IBD for pairs of study subjects, with prediction ellipses
for known relationships superposed, if requested by the user
with simulate=TRUE
.
The prediction ellipses are produced from estimated IBD coefficients
for a user-specified number (default 200) of simulated pairs of
known relationships, assuming the distribution of estimated
IBD coefficients is approximately bivariate Normal.
When simulated pairs are omitted (simulate=FALSE
),
plotting produces a single interactive display of estimated IBD
coefficients for pairs of study subjects specified by kinshipth
, on which points
may be identified by clicking with the mouse.
By contrast, when the IBD
object includes simulated pairs,
the function returns a series of plots, which the user is
prompted to view and interact with successively.
The first plot to appear is non-clickable and shows the
estimated IBD coefficients for pairs of study subjects
specified by kinshipth
,
along with the prediction ellipse for unrelated, simulated pairs.
Subsequent plots are clickable and correspond to each relationship
requested in the call to IBDcheck()
. These relationship-specific
plots are for identifying pairs of study subjects which could have the
relationship. The plotting regions are
restricted to the neighborhood of the prediction ellipse for
the simulated pairs of that relationship, which is also drawn.
If, however, the plotting region overlaps with the
prediction ellipse for simulated unrelated pairs,
the ellipse for simulated unrelated pairs is drawn as well.
Points falling within the
prediction ellipse for the relationship
and outside the prediction
ellipse for unrelated pairs are automatically flagged.
In addition,
users may click on points of study pairs that appear to be related
but are not automatically flagged.
The plot method produces a data frame of information on pairs
that have been flagged on the different plots,
either automatically or interactively by the user through
clicking the mouse.
Additional details:
The showLabels
function in the car package
is used to implement identification of points by left-clicking the
mouse on interactive plots.
When finished identifying points, users should
right-click the plotting region to move to the next plot.
A Bonferroni-type adjustment is applied when computing the ellipse for
unrelated pairs to account for the fact that, typically, most
study pairs will be unrelated. Specifically,
the coverage probability for the simulated unrelated
pairs ellipse is taken to be
1-(1-ellipse.coverage)/npairs, where
npairs is the number of pairs of study subjects.
A data frame of information on pairs that are flagged, either automatically or by user mouse-clicks, on the different plots provided by the function. The columns of this data frame are:
member1 |
ID of the first member of the study pair |
member2 |
ID of the second member of the study pair |
pz0 |
estimated proportion of markers with zero alleles IBD |
pz1 |
estimated proportion of markers with one allele IBD |
relationship |
If |
Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | data(Nhlsim)
## Not run:
# Example with simulate=FALSE (default)
popsam<-Nhlsim$csct==0 # controls
dat<-new.IBD(Nhlsim$snp.data,Nhlsim$chromosome,Nhlsim$physmap,popsam)
cibd<-IBDcheck(dat)
plot(cibd)
# Example with simulate=TRUE. Use chromosomes 20, 21 and 22 only.
cind<-(Nhlsim$chromosome == 20 | Nhlsim$chromosome == 21 | Nhlsim$chromosome == 22)
dat<-new.IBD(Nhlsim$snp.data[,cind],Nhlsim$chromosome[cind],
Nhlsim$physmap[cind],popsam)
ss<-sim.control(simulate=TRUE,fitLD=TRUE)
cibd2<-IBDcheck(dat,simparams=ss)
plot(cibd2)
# Example use of kinshipth argument: On the plot of study subjects, only plot
# those with kinship coefficient greater than the 99th percentile of the
# kinship coefficients of simulated unrelated individuals.
plot(cibd2,kinshipth="empirical")
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.