ctl: Correlated Trait Locus (CTL) Mapping in R
Version 1.0.0-0

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ctl")

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

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

Files

inst
inst/CITATION
inst/TODO.txt
inst/STATUS.txt
inst/README.txt
inst/doc
inst/doc/manual.pdf
inst/doc/manual.Rnw
inst/doc/manual.R
tests
tests/GeneExpression_Yeast_RBrem.R
tests/test_ctl_long.R
tests/GeneExpression_Yeast_Annotation.txt
tests/GeneExpression_Yeast_RBrem.csvr
src
src/matrix.c
src/permutation.h
src/vector.c
src/vector.h
src/sort.c
src/permutation.c
src/ctlio.h
src/mapctl.h
src/mapctl.c
src/structs.h
src/sort.h
src/rmapctl.c
src/structs.c
src/ctlio.c
src/rmapctl.h
src/correlation.c
src/ctl.h
src/matrix.h
src/correlation.h
NAMESPACE
data
data/ath.metabolites.RData
data/ath.churchill.RData
data/datalist
data/ath.result.RData
data/yeast.brem.RData
R
R/helper.functions.R
R/ctl.image.R
R/ctl.plot.R
R/ctl.print.R
R/ctl.power.R
R/ctl.sd.R
R/basic.qc.R
R/ctl.lineplot.R
R/ctl.network.R
R/ctl.utils.R
R/ctl.profiles.R
R/ctl.load.R
R/detect.peaks.R
R/ctl.correlation.R
R/ctl.circle.R
R/ctl.hist.R
R/ctl.slope.R
R/ctl.scan.R
R/plot.traits.R
R/zzz.R
R/ctl.statistics.R
vignettes
vignettes/prepare.bat
vignettes/manual.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/ctl.hist.Rd
man/scanSlopes.Rd
man/ctl.profiles.Rd
man/detect.peaks.Rd
man/ctl.image.Rd
man/scanSD.cross.Rd
man/basic.qc.Rd
man/scanSlopes.cross.Rd
man/ctl.helper.Rd
man/plotTraits.Rd
man/ctl.mapping.Rd
man/ctl.load.Rd
man/yeast.brem.Rd
man/ath.result.Rd
man/ctl.network.Rd
man/ctl.lineplot.Rd
man/ctl.regions.Rd
man/ath.churchill.Rd
man/ctl.scan.Rd
man/ctl.scan.cross.Rd
man/ctl.print.ctlobject.Rd
man/ctl.significant.Rd
man/ath.metabolites.Rd
man/ctl.print.ctlscan.Rd
man/ctl.plot.ctlobject.Rd
man/ctl.plot.ctlscan.Rd
man/ctl.circle.Rd
man/ctl-internal.Rd
man/qtl.image.Rd
man/ctl.permute.plot.Rd
man/ctl-package.Rd
man/scanSD.Rd
ctl documentation built on May 19, 2017, 10:19 p.m.