ctl: Correlated Trait Locus (CTL) Mapping in R

Analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL).

AuthorDanny Arends <Danny.Arends@gmail.com>
Date of publication2016-09-20 15:39:01
MaintainerDanny Arends <Danny.Arends@gmail.com>
LicenseGPL-3
Version1.0.0-0

View on CRAN

Man pages

ath.churchill: Example metabolite expression data from Arabidopsis Thaliana...

ath.metabolites: Example metabolite expression data from Arabidopsis Thaliana...

ath.result: Output of QCLscan after 5000 permutations on the metabolite...

basic.qc: Create quality control plots.

ctl.circle: Circleplot CTL on multiple traits

ctl.helper: CTLhelper - Helper functions for CTL mapping

ctl.hist: Plot histogram of CTL permutations

ctl.image: Plot genome-wide CTL on multiple traits

ctl-internal: Internal CTL functions

ctl.lineplot: Lineplot CTL on multiple traits

ctl.load: ctl.load - Load CTLs calculated by the D2.0 version

ctl.mapping: CTLmapping - Scan for correlated trait loci (CTL)

ctl.network: CTLnetwork - Interaction network from a genome-wide CTLscan...

ctl-package: CTL - CTL mapping in experimental crosses

ctl.permute.plot: Differential correlation versus likelihood plotted in curves

ctl.plot.ctlobject: Plot CTL curves or heatmaps

ctl.plot.ctlscan: Plot CTL results as bar, line or GWAS plot.

ctl.print.ctlobject: Print the results of a CTL genome scan

ctl.print.ctlscan: Print the results of a single phenotype CTL scan

ctl.profiles: CTLprofiles - Extract CTL interaction profiles

ctl.regions: CTLregions - Get all significant interactions from a...

ctl.scan: CTLscan - Scan for Correlated Trait Locus (CTL)

ctl.scan.cross: CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl...

ctl.significant: CTLsignificant - Get all significant interactions from a...

detect.peaks: detect.peaks - Peak detection algorithm to 'flatten' data...

plotTraits: plotTraits - Trait vs Trait scatterplot, colored by the...

qtl.image: Plot a QTL heatmap of the phenotypes scanned by CTLscan

scanSD: scanSD - Analyze the differences in Standard Deviation...

scanSD.cross: scanSD.cross - Analyze the differences in standard deviation...

scanSlopes: scanSlopes - Create a slope difference profile between two...

scanSlopes.cross: scanSlopes.cross - Create a slope difference profile between...

yeast.brem: Example gene expression data from Saccharomyces cerevisiae on...

Functions

addChromosomeLines Man page
a_loc Man page
ath.churchill Man page
ath.gary Man page
ath.metab Man page
ath.metabolites Man page
ath.result Man page
basic.qc Man page
check.genotypes Man page
check.marker Man page
check.pheno Man page
chiSQN Man page
chiSQtoP Man page
chr_length Man page
chr_total_length Man page
circle.loc Man page
correlated.phenotype Man page
correlation Man page
create.marker Man page
ctl Man page
CTL Man page
CTLanalyseEffects Man page
CTLanalyseRatios Man page
CTLasLOD Man page
ctl.circle Man page
ctl.ctlmatrix Man page
ctl.dcormatrix Man page
ctl.lineplot Man page
ctl.load Man page
CTLmapping Man page
ctl.name Man page
ctl.names Man page
CTLnetwork Man page
CTLnetwork.addmarker Man page
CTLpowerAnalysis Man page
CTLprofiles Man page
ctl.qtlmatrix Man page
ctl.qtlprofile Man page
CTLregions Man page
CTLscan Man page
CTLscan.cross Man page
CTLscantoScanone Man page
CTLsignificant Man page
CTLtoLODvector Man page
ctl.version Man page
dcor Man page
dcor.create Man page
deltaSD Man page
detect.peaks Man page
draw.element Man page
draw.spline Man page
dw Man page
extrapolateBeyondRange Man page
gcLoop Man page
get.chr.edges Man page
getCorrelations Man page
getCorrelations.cross Man page
getPermuteThresholds Man page
getRatio Man page
getRVM Man page
hist.CTLobject Man page
image.CTLobject Man page
internal.image Man page
lodscorestoscanone Man page
mapinfotomarkerlocs Man page
m_loc Man page
munique Man page
nfrom Man page
nto Man page
plot.CTLnetwork Man page
plot.CTLobject Man page
plot.CTLpermute Man page
plot.CTLscan Man page
plot.CTLscan2 Man page
plotCTLscan3 Man page
plotExpression Man page
plotTraits Man page
print.CTLobject Man page
print.CTLpermute Man page
print.CTLscan Man page
printSignificantSlope Man page
qtlimage Man page
redblue Man page
remove.diag Man page
scanSD Man page
scanSD.cross Man page
scanSlopes Man page
scanSlopes.cross Man page
stdSlopeBeta Man page
stdSlopeError Man page
stdSlopeEstimate Man page
stdSlopeIntercept Man page
stdSlopeTest Man page
test.chiSQN Man page
test.correlation Man page
test.getCorrelation.cross Man page
test.power.test Man page
top.correlated Man page
up Man page
whiteblack Man page
yeast.brem Man page

Files

ctl
ctl/inst
ctl/inst/CITATION
ctl/inst/TODO.txt
ctl/inst/STATUS.txt
ctl/inst/README.txt
ctl/inst/doc
ctl/inst/doc/manual.pdf
ctl/inst/doc/manual.Rnw
ctl/inst/doc/manual.R
ctl/tests
ctl/tests/GeneExpression_Yeast_RBrem.R
ctl/tests/test_ctl_long.R
ctl/tests/GeneExpression_Yeast_Annotation.txt
ctl/tests/GeneExpression_Yeast_RBrem.csvr
ctl/src
ctl/src/matrix.c
ctl/src/permutation.h
ctl/src/vector.c
ctl/src/vector.h
ctl/src/sort.c
ctl/src/permutation.c
ctl/src/ctlio.h
ctl/src/mapctl.h
ctl/src/mapctl.c
ctl/src/structs.h
ctl/src/sort.h
ctl/src/rmapctl.c
ctl/src/structs.c
ctl/src/ctlio.c
ctl/src/rmapctl.h
ctl/src/correlation.c
ctl/src/ctl.h
ctl/src/matrix.h
ctl/src/correlation.h
ctl/NAMESPACE
ctl/data
ctl/data/ath.metabolites.RData
ctl/data/ath.churchill.RData
ctl/data/datalist
ctl/data/ath.result.RData
ctl/data/yeast.brem.RData
ctl/R
ctl/R/helper.functions.R ctl/R/ctl.image.R ctl/R/ctl.plot.R ctl/R/ctl.print.R ctl/R/ctl.power.R ctl/R/ctl.sd.R ctl/R/basic.qc.R ctl/R/ctl.lineplot.R ctl/R/ctl.network.R ctl/R/ctl.utils.R ctl/R/ctl.profiles.R ctl/R/ctl.load.R ctl/R/detect.peaks.R ctl/R/ctl.correlation.R ctl/R/ctl.circle.R ctl/R/ctl.hist.R ctl/R/ctl.slope.R ctl/R/ctl.scan.R ctl/R/plot.traits.R ctl/R/zzz.R ctl/R/ctl.statistics.R
ctl/vignettes
ctl/vignettes/prepare.bat
ctl/vignettes/manual.Rnw
ctl/MD5
ctl/build
ctl/build/vignette.rds
ctl/DESCRIPTION
ctl/man
ctl/man/ctl.hist.Rd ctl/man/scanSlopes.Rd ctl/man/ctl.profiles.Rd ctl/man/detect.peaks.Rd ctl/man/ctl.image.Rd ctl/man/scanSD.cross.Rd ctl/man/basic.qc.Rd ctl/man/scanSlopes.cross.Rd ctl/man/ctl.helper.Rd ctl/man/plotTraits.Rd ctl/man/ctl.mapping.Rd ctl/man/ctl.load.Rd ctl/man/yeast.brem.Rd ctl/man/ath.result.Rd ctl/man/ctl.network.Rd ctl/man/ctl.lineplot.Rd ctl/man/ctl.regions.Rd ctl/man/ath.churchill.Rd ctl/man/ctl.scan.Rd ctl/man/ctl.scan.cross.Rd ctl/man/ctl.print.ctlobject.Rd ctl/man/ctl.significant.Rd ctl/man/ath.metabolites.Rd ctl/man/ctl.print.ctlscan.Rd ctl/man/ctl.plot.ctlobject.Rd ctl/man/ctl.plot.ctlscan.Rd ctl/man/ctl.circle.Rd ctl/man/ctl-internal.Rd ctl/man/qtl.image.Rd ctl/man/ctl.permute.plot.Rd ctl/man/ctl-package.Rd ctl/man/scanSD.Rd

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