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).

Author
Danny Arends <Danny.Arends@gmail.com>
Date of publication
2016-09-20 15:39:01
Maintainer
Danny Arends <Danny.Arends@gmail.com>
License
GPL-3
Version
1.0.0-0

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...

Files in this package

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