profileplot {dlmap} | R Documentation |
Plots the Wald statistic profile for each chromosome with detected QTL on first
interval mapping scan. Indicates marker locations, marker names, and detected
QTL positions obtained from a dlmap
fit.
profileplot(object, ...) ## S3 method for class 'dlmap': profileplot(object, chr, marker.names=TRUE, QTLpos=TRUE, pch=20, ...)
object |
object of class dlmap |
chr |
character string naming the subset of chromosomes to plot; or, if numeric, a vector of chromosome indices |
marker.names |
logical value. if TRUE then marker names are plotted along the top of the plot. Defaults to TRUE |
QTLpos |
logical value. if TRUE then QTL positions are indicated with vertical lines. Defaults to TRUE |
pch |
Character to be used for points in plotting; default is solid circle |
... |
arguments passed to "plot" to set up the plot region. Arguments may also be passed to "text" for the manipulation of the marker names |
The function profileplot
provides a neat visual display of
the Wald profile for chromosomes with detected QTL. If no QTL are detected,
nothing will be plotted. Otherwise, the Wald profile will be plotted by cM
position of points on the interval mapping grid. Marker names will be
displayed at the appropriate positions along the top of the plot. Vertical
lines will mark the position of detected QTL.
The Wald profile from the first iteration of interval mapping scans is plotted for all selected chromosomes, with marker names, marker locations, and QTL positions displayed.
Emma Huang and Andrew George; Julian Taylor
Huang, BE and George, AW. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911
## Not run: # load dataset data(BSdat) dl.in1 <- dlcross(format="rqtl", obj=BSdat, idname="ID", fixpos=1) BSdl <- dlmap.asreml(object=dl.in1, phename="phenotype", filestem="BS") BSdl <- dlmap.lme(object=dl.in1, phename="phenotype", filestem="BS") profileplot(BSdl) ## End(Not run)