qtlPlot {MetaNetwork} | R Documentation |
Plot QTL profiles.
qtlPlot(markers, qtlProfiles, qtlThres, addTitle=NULL, addMarkerLabels=F, addLegend=T, color=NULL)
Draws a plots that visualizes the -log_{10}(p) QTL values (y-axis) along the markers on the genome (x-axis), parameterized based on user-defined settings.
The markers
should be ordered sequentially.
The names of makers should be consistent over markers
and qtlProfiles
.
Jingyuan Fu <j.fu@rug.nl>, Morris Swertz <m.a.swertz@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>
Fu J, Swertz MA, Keurentjes JJB, Jansen RC. MetaNetwork: a computational tool for the genetic study of metabolism. Nature Protocols (2007).
http://gbic.biol.rug.nl/supplementary/2007/MetaNetwork
## load the example data provided with this package data(markers) data(genotypes) data(traits) ##OR: load your own data #markers <- loadData("markers.csv") #genotypes <- loadData("genotypes.csv") #traits <- loadData("traits.csv") ##calculate the two part qtl qtlProfiles <- qtlMapTwoPart(genotypes=genotypes, traits=traits, spike=4) ##set the qtl threshold qtlThres <- 3.79 ##OR: estimate the threshold yourself #qtlThres <- qtlThreshold(genotypes, traits, spike=4) ##plot the qtlProfiles qtlPlot(markers, qtlProfiles, qtlThres)