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ctl (version 1.0.0-0)
Correlated Trait Locus (CTL) Mapping in R
Description
Analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL).
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Install
install.packages('ctl')
Monthly Downloads
263
Version
1.0.0-0
License
GPL-3
Maintainer
Danny Arends
Last Published
September 20th, 2016
Functions in ctl (1.0.0-0)
Search functions
ctl.circle
Circleplot CTL on multiple traits
basic.qc
Create quality control plots.
ath.result
Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.
image.CTLobject
Plot genome-wide CTL on multiple traits
ath.churchill
Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.
CTLhelper
CTLhelper - Helper functions for CTL mapping
hist.CTLobject
Plot histogram of CTL permutations
ctl-internal
Internal CTL functions
ctl-package
CTL - CTL mapping in experimental crosses
ath.metabolites
Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.
plot.CTLpermute
Differential correlation versus likelihood plotted in curves
ctl.lineplot
Lineplot CTL on multiple traits
CTLnetwork
CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits
print.CTLscan
Print the results of a single phenotype CTL scan
plot.CTLobject
Plot CTL curves or heatmaps
plot.CTLscan
Plot CTL results as bar, line or GWAS plot.
ctl.load
ctl.load - Load CTLs calculated by the D2.0 version
CTLprofiles
CTLprofiles - Extract CTL interaction profiles
print.CTLobject
Print the results of a CTL genome scan
CTLmapping
CTLmapping - Scan for correlated trait loci (CTL)
detect.peaks
detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold
scanSlopes.cross
scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)
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)
CTLscan
CTLscan - Scan for Correlated Trait Locus (CTL)
qtlimage
Plot a QTL heatmap of the phenotypes scanned by CTLscan
CTLregions
CTLregions - Get all significant interactions from a genome-wide CTLscan
plotTraits
plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus
CTLsignificant
CTLsignificant - Get all significant interactions from a genome-wide CTLscan
CTLscan.cross
CTLscan.cross - Scan for Correlated Trait Locus (CTL) (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.