Correlated Trait Locus Mapping


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Documentation for package ‘ctl’ version 1.0.0-4

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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.