Plot QTL profiles

Description

Plot QTL profiles.

Usage

qtlPlot(markers, qtlProfiles, qtlThres, addTitle=NULL, addMarkerLabels=F, 
        addLegend=T, color=NULL)

Value

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.

Note

The markers should be ordered sequentially. The names of makers should be consistent over markers and qtlProfiles.

Author(s)

Jingyuan Fu <j.fu@rug.nl>, Morris Swertz <m.a.swertz@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>

References

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

Examples

## 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)