Package: ctl 1.0.0-10

ctl: Correlated Trait Locus Mapping

Identification and network inference of genetic loci associated with correlation changes in quantitative traits (called correlated trait loci, CTLs). Arends et al. (2016) <doi:10.21105/joss.00087>.

Authors:Danny Arends <[email protected]>, Yang Li, Gudrun A Brockmann, Ritsert C Jansen, Robert W Williams, and Pjotr Prins

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ctl_1.0.0-10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ctl/json (API)

# Install 'ctl' in R:

install.packages('ctl', repos = c('https://dannyarends.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openmp– GCC OpenMP (GOMP) support library

Datasets:

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.
yeast.brem - Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openmp

3.46 score 143 scripts 373 downloads 2 mentions 93 exports 2 dependencies

Last updated from:51422439e8. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	91
linux-devel-x86_64	OK	105
source / vignettes	OK	142
linux-release-arm64	OK	90
linux-release-x86_64	OK	108
macos-release-arm64	OK	161
macos-release-x86_64	OK	416
macos-oldrel-arm64	OK	193
macos-oldrel-x86_64	OK	410
windows-devel-arm64	OK	417
windows-devel-x86_64	OK	127
windows-release-arm64	OK	419
windows-release-x86_64	OK	101
windows-oldrel-x86_64	OK	109
wasm-release	OK	85

Exports:a_loc addChromosomeLines basic.qc check.genotypes check.marker check.pheno chiSQN chiSQtoP chr_length chr_total_length circle.loc correlated.phenotype correlation create.marker ctl.circle ctl.ctlmatrix ctl.dcormatrix ctl.lineplot ctl.load ctl.name ctl.names ctl.qtlmatrix ctl.qtlprofile ctl.version CTLanalyseEffects CTLanalyseRatios CTLasLOD ctleffects CTLmapping ctlmarker CTLnetwork CTLnetwork.addmarker CTLpowerAnalysis CTLprofiles CTLregions CTLscan CTLscan.cross CTLscantoScanone CTLsignificant CTLtoLODvector dcor dcor.create deltaSD detect.peaks draw.element draw.spline gcLoop get.chr.edges getCorrelations getCorrelations.cross getPermuteThresholds getRatio getRVM hist.CTLobject image.CTLobject internal.image lodscorestoscanone m_loc mapinfotomarkerlocs munique nfrom nto openmp plot.CTLnetwork plot.CTLobject plot.CTLpermute plot.CTLscan plotCTLscan3 plotExpression plotTraits print.CTLobject print.CTLpermute print.CTLscan printSignificantSlope qtlimage QTLmapping redblue remove.diag scanSD scanSD.cross scanSlopes scanSlopes.cross stdSlopeBeta stdSlopeError stdSlopeEstimate stdSlopeIntercept stdSlopeTest test.chiSQN test.correlation test.getCorrelation.cross test.power.test top.correlated whiteblack

Dependencies:MASS qtl

Manual

Rendered frommanual.Rnwusingutils::Sweave

Last update: 2023-11-28
Started: 2016-09-20

Citation

Readme and manuals

Help Manual

Help page	Topics
CTL - CTL mapping in experimental crosses	CTL ctl
Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.	ath.churchill ath.gary
Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.	ath.metab ath.metabolites
Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.	ath.result
Create quality control plots.	basic.qc
Circleplot CTL on multiple traits	ctl.circle
Lineplot CTL on multiple traits	ctl.lineplot
ctl.load - Load CTLs calculated by the D2.0 version	ctl.load
CTLhelper - Helper functions for CTL mapping	ctl.ctlmatrix ctl.dcormatrix ctl.name ctl.names ctl.qtlmatrix ctl.qtlprofile
CTLmapping - Scan for correlated trait loci (CTL)	CTLmapping
CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits	CTLnetwork
CTLprofiles - Extract CTL interaction profiles	CTLprofiles
CTLregions - Get all significant interactions from a genome-wide CTLscan	CTLregions
CTLscan - Scan for Correlated Trait Locus (CTL)	CTLscan
CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object)	CTLscan.cross
CTLsignificant - Get all significant interactions from a genome-wide CTLscan	CTLsignificant
detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold	detect.peaks
Plot histogram of CTL permutations	hist.CTLobject
Plot genome-wide CTL on multiple traits	image.CTLobject
Plot CTL curves or heatmaps	plot.CTLobject
Differential correlation versus likelihood plotted in curves	plot.CTLpermute
Plot CTL results as bar, line or GWAS plot.	plot.CTLscan
plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus	plotTraits
Print the results of a CTL genome scan	print.CTLobject
Print the results of a single phenotype CTL scan	print.CTLscan
Plot a QTL heatmap of the phenotypes scanned by CTLscan	qtlimage
QTLmapping - QTL mapping method for CTL analysis	QTLmapping
scanSD - Analyze the differences in Standard Deviation between genotypes between two traits	scanSD
scanSD.cross - Analyze the differences in standard deviation between two traits at a certain genetic marker (R/qtl cross object)	scanSD.cross
scanSlopes - Create a slope difference profile between two traits	scanSlopes
scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)	scanSlopes.cross
Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.	yeast.brem

Package: ctl 1.0.0-10

ctl: Correlated Trait Locus Mapping

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)