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ctl (version 1.0.0-10)
Correlated Trait Locus Mapping
Description
Identification and network inference of genetic loci associated with correlation changes in quantitative traits (called correlated trait loci, CTLs). Arends et al. (2016)
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Install
install.packages('ctl')
Monthly Downloads
265
Version
1.0.0-10
License
GPL-3
Maintainer
Danny Arends
Last Published
January 16th, 2024
Functions in ctl (1.0.0-10)
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plot.CTLscan
Plot CTL results as bar, line or GWAS plot.
print.CTLscan
Print the results of a single phenotype CTL scan
plot.CTLpermute
Differential correlation versus likelihood plotted in curves
print.CTLobject
Print the results of a CTL genome scan
CTLmapping
CTLmapping - Scan for correlated trait loci (CTL)
plot.CTLobject
Plot CTL curves or heatmaps
CTLnetwork
CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits
CTLprofiles
CTLprofiles - Extract CTL interaction profiles
scanSD
scanSD - Analyze the differences in Standard Deviation between genotypes between two traits
ctl.load
ctl.load - Load CTLs calculated by the D2.0 version
ctl.lineplot
Lineplot CTL on multiple traits
QTLmapping
QTLmapping - QTL mapping method for CTL analysis
qtlimage
Plot a QTL heatmap of the phenotypes scanned by CTLscan
CTLscan
CTLscan - Scan for Correlated Trait Locus (CTL)
CTLregions
CTLregions - Get all significant interactions from a genome-wide CTLscan
scanSD.cross
scanSD.cross - Analyze the differences in standard deviation between two traits at a certain genetic marker (R/qtl cross object)
scanSlopes.cross
scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)
scanSlopes
scanSlopes - Create a slope difference profile between two traits
yeast.brem
Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.
detect.peaks
detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold
CTLsignificant
CTLsignificant - Get all significant interactions from a genome-wide CTLscan
plotTraits
plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus
CTLscan.cross
CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object)
ctl-package
CTL - CTL mapping in experimental crosses
hist.CTLobject
Plot histogram of CTL permutations
image.CTLobject
Plot genome-wide CTL on multiple traits
CTLhelper
CTLhelper - Helper functions for CTL mapping
ctl-internal
Internal CTL functions
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.
ath.churchill
Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.
ctl.circle
Circleplot CTL on multiple traits