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.pdf |ctl.html✨
ctl/json (API)

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

Peer review:

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.

93 exports 0.91 score 2 dependencies 2 mentions 103 scripts 351 downloads

Last updated 8 months agofrom:51422439e8. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-win-x86_64OKSep 13 2024
R-4.5-linux-x86_64OKSep 13 2024
R-4.4-win-x86_64OKSep 13 2024
R-4.4-mac-x86_64OKSep 13 2024
R-4.4-mac-aarch64OKSep 13 2024
R-4.3-win-x86_64OKSep 13 2024
R-4.3-mac-x86_64OKSep 13 2024
R-4.3-mac-aarch64OKSep 13 2024

Exports:a_locaddChromosomeLinesbasic.qccheck.genotypescheck.markercheck.phenochiSQNchiSQtoPchr_lengthchr_total_lengthcircle.loccorrelated.phenotypecorrelationcreate.markerctl.circlectl.ctlmatrixctl.dcormatrixctl.lineplotctl.loadctl.namectl.namesctl.qtlmatrixctl.qtlprofilectl.versionCTLanalyseEffectsCTLanalyseRatiosCTLasLODctleffectsCTLmappingctlmarkerCTLnetworkCTLnetwork.addmarkerCTLpowerAnalysisCTLprofilesCTLregionsCTLscanCTLscan.crossCTLscantoScanoneCTLsignificantCTLtoLODvectordcordcor.createdeltaSDdetect.peaksdraw.elementdraw.splinegcLoopget.chr.edgesgetCorrelationsgetCorrelations.crossgetPermuteThresholdsgetRatiogetRVMhist.CTLobjectimage.CTLobjectinternal.imagelodscorestoscanonem_locmapinfotomarkerlocsmuniquenfromntoopenmpplot.CTLnetworkplot.CTLobjectplot.CTLpermuteplot.CTLscanplotCTLscan3plotExpressionplotTraitsprint.CTLobjectprint.CTLpermuteprint.CTLscanprintSignificantSlopeqtlimageQTLmappingredblueremove.diagscanSDscanSD.crossscanSlopesscanSlopes.crossstdSlopeBetastdSlopeErrorstdSlopeEstimatestdSlopeInterceptstdSlopeTesttest.chiSQNtest.correlationtest.getCorrelation.crosstest.power.testtop.correlatedwhiteblack

Dependencies:MASSqtl

Manual

Rendered frommanual.Rnwusingutils::Sweaveon Sep 13 2024.

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

Readme and manuals

Help Manual

Help pageTopics
CTL - CTL mapping in experimental crossesCTL 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 traitsctl.circle
Lineplot CTL on multiple traitsctl.lineplot
ctl.load - Load CTLs calculated by the D2.0 versionctl.load
CTLhelper - Helper functions for CTL mappingctl.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 traitsCTLnetwork
CTLprofiles - Extract CTL interaction profilesCTLprofiles
CTLregions - Get all significant interactions from a genome-wide CTLscanCTLregions
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 CTLscanCTLsignificant
detect.peaks - Peak detection algorithm to 'flatten' data above a certain thresholddetect.peaks
Plot histogram of CTL permutationshist.CTLobject
Plot genome-wide CTL on multiple traitsimage.CTLobject
Plot CTL curves or heatmapsplot.CTLobject
Differential correlation versus likelihood plotted in curvesplot.CTLpermute
Plot CTL results as bar, line or GWAS plot.plot.CTLscan
plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locusplotTraits
Print the results of a CTL genome scanprint.CTLobject
Print the results of a single phenotype CTL scanprint.CTLscan
Plot a QTL heatmap of the phenotypes scanned by CTLscanqtlimage
QTLmapping - QTL mapping method for CTL analysisQTLmapping
scanSD - Analyze the differences in Standard Deviation between genotypes between two traitsscanSD
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 traitsscanSlopes
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