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ctl (version 1.0.0-2)
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
280
Version
1.0.0-2
License
GPL-3
Maintainer
Danny Arends
Last Published
August 3rd, 2018
Functions in ctl (1.0.0-2)
Search functions
ctl.lineplot
Lineplot CTL on multiple traits
plot.CTLscan
Plot CTL results as bar, line or GWAS plot.
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
ctl.load
ctl.load - Load CTLs calculated by the D2.0 version
print.CTLscan
Print the results of a single phenotype CTL scan
detect.peaks
detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold
yeast.brem
Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.
print.CTLobject
Print the results of a CTL genome scan
plotTraits
plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus
CTLprofiles
CTLprofiles - Extract CTL interaction profiles
plot.CTLpermute
Differential correlation versus likelihood plotted in curves
ath.metabolites
Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.
qtlimage
Plot a QTL heatmap of the phenotypes scanned by CTLscan
CTLmapping
CTLmapping - Scan for correlated trait loci (CTL)
QTLmapping
QTLmapping - QTL mapping method for CTL analysis
plot.CTLobject
Plot CTL curves or heatmaps
CTLnetwork
CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits
CTLregions
CTLregions - Get all significant interactions from a genome-wide CTLscan
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)
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)
ctl.circle
Circleplot CTL on multiple traits
basic.qc
Create quality control plots.
hist.CTLobject
Plot histogram of CTL permutations
CTLhelper
CTLhelper - Helper functions for CTL mapping
ctl-internal
Internal CTL functions
image.CTLobject
Plot genome-wide CTL on multiple traits
ath.result
Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.
ath.churchill
Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.
ctl-package
CTL - CTL mapping in experimental crosses