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...

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

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