pheno2geno: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains
Version 1.3.1

High-throughput generation of genetic markers from molecular phenotypes for crosses between inbred strains. These markers can be use to saturate existing genetic map or creating a new one.

AuthorKonrad Zych <k.zych@rug.nl> and Danny Arends <danny.arends@gmail.com>
Date of publication2015-03-25 16:08:51
MaintainerKonrad Zych <k.zych@rug.nl>
LicenseGPL-3
Version1.3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pheno2geno")

Getting started

README.md

Popular man pages

changeChromNumber: Change the number of chromosomes in a cross object
fake.population: Simulate a population object.
findDiffExpressed: Finding differentially expressed genes.
find.mixups: Find sample mix-ups
generate.biomarkers: Generate discrete biomarkers from the continuous phenotypes
markerPlacementPlot: Plot number of markers selected.
plotChildrenExpression: Plotting routine for children expression data.
See all...

All man pages Function index File listing

Man pages

add.to.population: Add additional data to a population object
assignedChrToMarkers: Function that assigns a chromosome label to a genetic marker
changeChromNumber: Change the number of chromosomes in a cross object
create.population: Create a population object
cross.denovo: Create a de novo genetic map from a population object.
cross.saturate: Saturate an existing genetic map.
fake.population: Simulate a population object.
findDiffExpressed: Finding differentially expressed genes.
find.mixups: Find sample mix-ups
generate.biomarkers: Generate discrete biomarkers from the continuous phenotypes
map.functions: Functions to provide some descriptive statistics on genetic...
markerPlacementPlot: Plot number of markers selected.
markersCorPlot: Plotting correlation between markers on two maps.
phenotypes2genotypes-internal: Internal pheno2geno functions
phenotypes2genotypes-package: Pheno2Geno - High-throughput generation of genetic markers...
plotChildrenExpression: Plotting routine for children expression data.
plotMapComparison: Plotting routine for comparison of two genetic maps.
plotMarkerDistribution: plotMarkerDistribution
plotParentalExpression: Plotting routine for parental expression data.
power.plot: Comparison of power of qtl detection.
projectOldMarkers: Plotting routine which shows where markers from original map...
pull.biomarkers: Extract the detected biomarkers from a population object.
qtl.comparison.plot: Comparison of qtl profiles.
read.population: Loading genotype and phenotype data
reorganizeMarkersWithin: Reorganize markers within cross object.
RPpval: Visualize the outcome of a Rank product analysis
save.gff: Saving gff files.
scan.qtls: Scan qtls
set.geno.from.cross: Pull genotype from an object of class cross.
testCross: Test cross object
testPopulation: Test population object
transformations: Basic functions to do transformation / normalization of...
write.population: Writes a population object to file.

Functions

add.to.population Man page Source code
add.to.populationSub.internal Man page Source code
add.to.populationSubAnnots.internal Man page Source code
add.to.populationSubGeno.internal Man page Source code
add.to.populationSubMap.internal Man page Source code
add.to.populationSubPheno.internal Man page Source code
analyseLineVariance Man page Source code
applyFunctionToFile Man page Source code
ascendingMaptoJigSawMap Man page Source code
assignChrToMarkers Man page Source code
assignLinkageGroups Man page Source code
assignMaximum Man page Source code
assignMaximumNoConflicts Man page Source code
avg_map_distances Man page Source code
bestCorelated.internal Man page Source code
bestCorelatedSub.internal Man page Source code
bestQTL.internal Man page Source code
bestQTLSub.internal Man page Source code
check.population Man page Source code
checkAndBind Man page Source code
checkForEpistasis Man page Source code
chromosomesLengths.internal Man page Source code
cleanGeno.internal Man page Source code
cleanNames.internal Man page Source code
cleanRfs Man page Source code
coloringMode Man page
convertMap.internal Man page Source code
convertType.internal Man page Source code
create.population Man page Source code
createMix Man page Source code
createMix.test Man page Source code
cross.denovo Man page Source code
cross.denovo.internal Man page Source code
cross.saturate Man page Source code
dataObject Man page
dataType Man page
defaultCheck.internal Man page Source code
doCleanUp.internal Man page Source code
donothing Man page Source code
fake.population Man page Source code
fakeFounders.internal Man page Source code
fakeMixUps.internal Man page Source code
fakePheno.internal Man page Source code
fakePhysicalMap.internal Man page Source code
filterRow.internal Man page Source code
find.diff.expressed Man page Source code
find.mixups Man page Source code
findUsingTTest.internal Man page Source code
fullScanRow.internal Man page Source code
generate.biomarkers Man page Source code
generate.biomarkers.internal Man page Source code
genotypeCheck.internal Man page Source code
genotypesToCross.internal Man page Source code
getChrOffsets.internal Man page Source code
getChromosome.internal Man page Source code
getMarkerOffsets Man page Source code
getMarkerOffsets.internal Man page
getMarkerOffsetsFromMap Man page Source code
getPopulationOffsets.internal Man page Source code
getYLocs.internal Man page Source code
getpeaks.internal Man page Source code
groupLabels Man page
inListCheck.internal Man page
inRangeCheck.internal Man page
insertMarkers.internal Man page Source code
invertChromosome.internal Man page Source code
is.integer0 Man page Source code
logarithmic Man page
lowerTrng.internal Man page Source code
majorityCorrelation Man page Source code
majorityOfMarkers Man page Source code
makeChromPal.internal Man page Source code
makeHaplos.internal Man page Source code
map2mapCorrelationMatrix Man page Source code
map2mapImage Man page Source code
mapMarkers.internal Man page Source code
map_distances Man page Source code
margin Man page
markerPlacementPlot Man page Source code
markers Man page
markersCorPlot Man page Source code
matchMarkers Man page Source code
meanCorrelation Man page Source code
mergeChromosomes.internal Man page Source code
mergeEnv.internal Man page Source code
mergeInverted Man page Source code
mlog Man page Source code
mlogit Man page Source code
mprobit Man page Source code
msqrt Man page Source code
normalModeReading Man page Source code
numericCheck.internal Man page Source code
overlapInd Man page
pheno2geno Man page
phenotypeRow Man page
plot4Nmixture Man page Source code
plotChildrenExpression Man page Source code
plotMapComparison Man page Source code
plotMarkerDistribution Man page Source code
plotParentalExpression Man page Source code
plotRPpval Man page Source code
population Man page
power.plot Source code
power.plot Man page
print.population Man page Source code
printGeno.internal Man page Source code
processInteractions Man page Source code
projectOldMarkers Man page Source code
proportion Man page
pull.biomarkers Man page Source code
qtl.comparison.plot Man page Source code
read.population Man page Source code
readSingleFile Man page Source code
rearrangeMarkers Man page Source code
reciproce Man page Source code
reduceChromosomesNumber Man page Source code
removeChromosomes Man page Source code
removeChromosomesSub.internal Man page Source code
removeTooSmallChromosomes Man page Source code
reorganizeMarkersWithin Man page Source code
save.gff Man page Source code
scan.qtls Man page Source code
scoreMixups.internal Man page Source code
selectByLine Man page Source code
selectByLineApply Man page Source code
selectChr Man page Source code
selectPhenotypes Man page Source code
selectTopMarker.internal Man page Source code
set.geno.from.cross Man page Source code
showRPpval Man page Source code
simBC.internal Man page Source code
simulateParentalPhenotypes Man page Source code
splitPheno.Apply Man page Source code
splitPheno.internal Man page Source code
splitPhenoRowEM.internal Man page Source code
sumMajorityCorrelation Man page Source code
switchChromosomes.internal Man page Source code
tTestByLine Man page Source code
tTestByLineApply Man page Source code
testCross Man page
testPopulation Man page
transformation Man page Source code
twoGenosModel Man page Source code
write.population Man page Source code
writeGenotypes.internal Man page Source code
writePhenotypes.internal Man page Source code
writeSingleFile Man page Source code

Files

inst
inst/BUGS.txt
inst/CITATION
inst/TODO.txt
tests
tests/1k
tests/1k/maps_genetic.txt
tests/1k/offspring_annotations.txt
tests/1k/offspring_phenotypes.txt
tests/1k/test.r
tests/1k/offspring_genotypes.txt
tests/parental_phenotypes.csv
tests/map.csv
tests/offspring_phenotypes.csv
tests/test_analysis.R
tests/genotypes.csv
tests/mycross.csv
NAMESPACE
data
data/datalist
data/testPopulation.rda
data/testCross.rda
R
R/markersCorPlot.R
R/create.population.r
R/transformations.R
R/cross.denovo.R
R/read.population.R
R/plotRoutines.R
R/cross.saturate.R
R/save.gff.R
R/qtl.comparison.plot.R
R/plotMapComparison.R
R/utilities.R
R/fake.population.R
R/write.population.R
R/scan.qtls.r
R/postprocessing.R
R/power.plot.R
R/markerPlacementPlot.R
R/find.mixups.R
R/generate.biomarkers.R
R/checks.R
R/assignLinkageGroups.R
R/findDiffExpressed.R
R/genotypesToCross.R
R/map.functions.R
R/create.mixtures.R
R/add.to.population.R
README.md
MD5
DESCRIPTION
man
man/phenotypes2genotypes-internal.rd
man/testCross.rd
man/plotChildrenExpression.rd
man/phenotypes2genotypes-package.rd
man/plotParentalExpression.rd
man/changeChromNumber.rd
man/reorganizeMarkersWithin.rd
man/markersCorPlot.rd
man/pull.biomarkers.rd
man/transformations.rd
man/find.mixups.rd
man/assignedChrToMarkers.rd
man/cross.denovo.rd
man/findDiffExpressed.rd
man/write.population.rd
man/qtl.comparison.plot.rd
man/projectOldMarkers.rd
man/RPpval.rd
man/map.functions.rd
man/add.to.population.rd
man/fake.population.rd
man/scan.qtls.rd
man/read.population.rd
man/plotMarkerDistribution.rd
man/save.gff.rd
man/set.geno.from.cross.rd
man/testPopulation.rd
man/cross.saturate.rd
man/markerPlacementPlot.rd
man/generate.biomarkers.rd
man/plotMapComparison.rd
man/create.population.rd
man/power.plot.rd
pheno2geno documentation built on May 19, 2017, 1:38 p.m.

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