polySegratio: Simulate and test marker dosage for dominant markers in autopolyploids

Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.

Author
Peter Baker
Date of publication
2014-03-06 07:37:23
Maintainer
Peter Baker <p.baker1@uq.edu.au>
License
GPL-3
Version
0.2-4

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Man pages

addMisclass
Misclassifies marker data in objects of class autoMarker or...
addMissing
Adds missing data to objects of class autoMarker or autoCross
autoFill
Automatically fill out blanks of a vector with the preceding...
divide.autoMarkers
Divide markers by parental type
divideAutoMarkers
S3 class divideAutoMarkers
expected.segRatio
Compute theoretical segregation proportions for regular...
makeLabel
Generate labels from two columns where blanks in first column...
plot.segRatio
Plot segregation ratios for either observed or simulated...
polySegratio-package
Segregation ratios for autoployploids
print.segRatio
Print segregation ratios
print.simAutoMarkers
Print objects of class simAutoMarkers
print.testSegRatio
Print objects of class testSegRatio
segRatio
S3 class segRatio
segregationRatios
Compute observed segregation proportions for dominant markers...
sim.autoCross
Simulate dominant markers for an autopolyploid cross for all...
simAutoCross
S3 class simAutoCross
sim.autoMarkers
Simulates dominant markers from an autopolyploid cross
simAutoMarkers
S3 class simAutoMarkers
test.segRatio
Classic tests for assessing marker dosage in autopolyploids
testSegRatio
S3 class testSegRatio

Files in this package

polySegratio/CHANGELOG
polySegratio/DESCRIPTION
polySegratio/NAMESPACE
polySegratio/R
polySegratio/R/addMisclass.R
polySegratio/R/addMissing.R
polySegratio/R/autoFill.R
polySegratio/R/divide.autoMarkers.R
polySegratio/R/expected.segRatio.R
polySegratio/R/makeLabel.R
polySegratio/R/plot.segRatio.R
polySegratio/R/plot.simAutoCross.R
polySegratio/R/plot.simAutoMarkers.R
polySegratio/R/print.divideAutoMarkers.R
polySegratio/R/print.segRatio.R
polySegratio/R/print.simAutoCross.R
polySegratio/R/print.simAutoMarkers.R
polySegratio/R/print.testSegRatio.R
polySegratio/R/segregationRatios.R
polySegratio/R/sim.autoCross.R
polySegratio/R/sim.autoMarkers.R
polySegratio/R/test.segRatio.R
polySegratio/build
polySegratio/build/vignette.rds
polySegratio/inst
polySegratio/inst/doc
polySegratio/inst/doc/polySegratio-overview.R
polySegratio/inst/doc/polySegratio-overview.Rnw
polySegratio/inst/doc/polySegratio-overview.pdf
polySegratio/man
polySegratio/man/addMisclass.Rd
polySegratio/man/addMissing.Rd
polySegratio/man/autoFill.Rd
polySegratio/man/divide.autoMarkers.Rd
polySegratio/man/divideAutoMarkers.Rd
polySegratio/man/expected.segRatio.Rd
polySegratio/man/makeLabel.Rd
polySegratio/man/plot.segRatio.Rd
polySegratio/man/polySegratio-package.Rd
polySegratio/man/print.segRatio.Rd
polySegratio/man/print.simAutoMarkers.Rd
polySegratio/man/print.testSegRatio.Rd
polySegratio/man/segRatio.Rd
polySegratio/man/segregationRatios.Rd
polySegratio/man/sim.autoCross.Rd
polySegratio/man/sim.autoMarkers.Rd
polySegratio/man/simAutoCross.Rd
polySegratio/man/simAutoMarkers.Rd
polySegratio/man/test.segRatio.Rd
polySegratio/man/testSegRatio.Rd
polySegratio/vignettes
polySegratio/vignettes/auto
polySegratio/vignettes/auto/polySegratio-overview.el
polySegratio/vignettes/polySeg.bib
polySegratio/vignettes/polySegratio-overview.Rnw
polySegratio/vignettes/tmp
polySegratio/vignettes/tmp/tmp-006.eps
polySegratio/vignettes/tmp/tmp-006.pdf
polySegratio/vignettes/tmp/tmp-007.eps
polySegratio/vignettes/tmp/tmp-007.pdf
polySegratio/vignettes/tmp/tmp-009.eps
polySegratio/vignettes/tmp/tmp-009.pdf
polySegratio/vignettes/tmp/tmp-010.eps
polySegratio/vignettes/tmp/tmp-010.pdf