polySegratio: Simulate and test marker dosage for dominant markers in autopolyploids
Version 0.2-4

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.

AuthorPeter Baker
Date of publication2014-03-06 22:09:55
MaintainerPeter Baker <p.baker1@uq.edu.au>
LicenseGPL-3
Version0.2-4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("polySegratio")

Getting started

Package overview

Popular man pages

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
segregationRatios: Compute observed segregation proportions for dominant markers...
sim.autoMarkers: Simulates dominant markers from an autopolyploid cross
simAutoMarkers: S3 class simAutoMarkers
See all...

All man pages Function index File listing

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

Functions

addMisclass Man page
addMissing Man page
autoFill Man page
divide.autoMarkers Man page
divideAutoMarkers Man page
expected.segRatio Man page
makeLabel Man page
plot.segRatio Man page
plot.simAutoCross Man page
plot.simAutoMarkers Man page
polySegratio Man page
polySegratio-package Man page
print.divideAutoMarkers Man page
print.segRatio Man page
print.simAutoCross Man page
print.simAutoMarkers Man page
print.testSegRatio Man page
segRatio Man page
segregationRatios Man page
sim.autoCross Man page
sim.autoMarkers Man page
simAutoCross Man page
simAutoMarkers Man page
test.segRatio Man page
testSegRatio Man page

Files

inst
inst/doc
inst/doc/polySegratio-overview.R
inst/doc/polySegratio-overview.pdf
inst/doc/polySegratio-overview.Rnw
NAMESPACE
CHANGELOG
R
R/print.testSegRatio.R
R/divide.autoMarkers.R
R/plot.segRatio.R
R/plot.simAutoMarkers.R
R/sim.autoCross.R
R/segregationRatios.R
R/makeLabel.R
R/plot.simAutoCross.R
R/addMisclass.R
R/autoFill.R
R/test.segRatio.R
R/print.simAutoMarkers.R
R/addMissing.R
R/print.segRatio.R
R/expected.segRatio.R
R/sim.autoMarkers.R
R/print.divideAutoMarkers.R
R/print.simAutoCross.R
vignettes
vignettes/polySeg.bib
vignettes/auto
vignettes/auto/polySegratio-overview.el
vignettes/tmp
vignettes/tmp/tmp-006.eps
vignettes/tmp/tmp-010.eps
vignettes/tmp/tmp-010.pdf
vignettes/tmp/tmp-006.pdf
vignettes/tmp/tmp-009.pdf
vignettes/tmp/tmp-009.eps
vignettes/tmp/tmp-007.pdf
vignettes/tmp/tmp-007.eps
vignettes/polySegratio-overview.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/makeLabel.Rd
man/print.segRatio.Rd
man/simAutoMarkers.Rd
man/test.segRatio.Rd
man/sim.autoCross.Rd
man/addMisclass.Rd
man/expected.segRatio.Rd
man/polySegratio-package.Rd
man/autoFill.Rd
man/addMissing.Rd
man/print.simAutoMarkers.Rd
man/sim.autoMarkers.Rd
man/testSegRatio.Rd
man/segregationRatios.Rd
man/print.testSegRatio.Rd
man/segRatio.Rd
man/divideAutoMarkers.Rd
man/plot.segRatio.Rd
man/divide.autoMarkers.Rd
man/simAutoCross.Rd
polySegratio documentation built on May 20, 2017, 12:42 a.m.