# Correlated Trait Locus Mapping

## Documentation for package ‘ctl’ version 1.0.0-4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ath.churchill | Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.
ath.gary | Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.
ath.metab | Example metabolite expression data from Arabidopsis Thaliana on 24 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 | CTL - CTL mapping in experimental crosses
ctl.circle | Circleplot CTL on multiple traits
ctl.ctlmatrix | CTLhelper - Helper functions for CTL mapping
ctl.dcormatrix | CTLhelper - Helper functions for CTL mapping
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
ctl.names | CTLhelper - Helper functions for CTL mapping
ctl.qtlmatrix | CTLhelper - Helper functions for CTL mapping
ctl.qtlprofile | CTLhelper - Helper functions for CTL mapping
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
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
QTLmapping | QTLmapping - QTL mapping method for CTL analysis
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.