CTLmapping              CTLmapping - Scan for correlated trait loci
                        (CTL)
CTLnetwork              CTLnetwork - Interaction network from a
                        genome-wide CTLscan of multiple traits
CTLprofiles             CTLprofiles - Extract CTL interaction profiles
CTLregions              CTLregions - Get all significant interactions
                        from a genome-wide CTLscan
CTLscan                 CTLscan - Scan for Correlated Trait Locus (CTL)
CTLscan.cross           CTLscan.cross - Scan for Correlated Trait Locus
                        (CTL) (R/qtl cross object)
CTLsignificant          CTLsignificant - Get all significant
                        interactions from a genome-wide CTLscan
ath.churchill           Example metabolite expression data from
                        Arabidopsis Thaliana on 9 metabolites.
ath.metabolites         Example metabolite expression data from
                        Arabidopsis Thaliana on 24 metabolites.
ath.result              Output of QCLscan after 5000 permutations on
                        the metabolite expression data from Arabidopsis
                        Thaliana.
basic.qc                Create quality control plots.
ctl                     CTL - CTL mapping in experimental crosses
ctl.circle              Circleplot CTL on multiple traits
ctl.lineplot            Lineplot CTL on multiple traits
ctl.load                ctl.load - Load CTLs calculated by the D2.0
                        version
ctl.name                CTLhelper - Helper functions for CTL mapping
detect.peaks            detect.peaks - Peak detection algorithm to
                        'flatten' data above a certain threshold
hist.CTLobject          Plot histogram of CTL permutations
image.CTLobject         Plot genome-wide CTL on multiple traits
plot.CTLobject          Plot CTL curves or heatmaps
plot.CTLpermute         Differential correlation versus likelihood
                        plotted in curves
plot.CTLscan            Plot CTL results as bar, line or GWAS plot.
plotTraits              plotTraits - Trait vs Trait scatterplot,
                        colored by the selected genetic locus
print.CTLobject         Print the results of a CTL genome scan
print.CTLscan           Print the results of a single phenotype CTL
                        scan
qtlimage                Plot a QTL heatmap of the phenotypes scanned by
                        CTLscan
scanSD                  scanSD - Analyze the differences in Standard
                        Deviation between genotypes between two traits
scanSD.cross            scanSD.cross - Analyze the differences in
                        standard deviation between two traits at a
                        certain genetic marker (R/qtl cross object)
scanSlopes              scanSlopes - Create a slope difference profile
                        between two traits
scanSlopes.cross        scanSlopes.cross - Create a slope difference
                        profile between two traits (R/qtl cross object)
yeast.brem              Example gene expression data from Saccharomyces
                        cerevisiae on 301 RNA expressions.
