Correlated Trait Locus Mapping

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Documentation for package ‘ctl’ version 1.0.0-10

• 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.