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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)

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