polySegratio (version 0.2-5)

polySegratio-package: Segregation Ratios for Autoployploids

Description

These functions provide tools for computing expected segregation ratios (or more correctly segregation proportions) for dominant markers in regular autopolyploids and simulating such marker data as well as conducting standard Chi squared tests and Binomial confidance intervals for assigning marker dosage.

Details

Package:	polySegratio
Type:	Package
Version:	0.2-5
Date:	2018-03-22
License:	GPL-3

Use expected.segRatio to compute expected segregation proportions for regular autopolyploids

Use segregationRatios to compute segregation ratios for a matrix of markers

Use test.segRatio to assignmarker dosage via Chi squared tests or Binomial CIs

Use sim.autoMarkers and sim.autoCross to simulate marker data under various scenarios

Use addMisclass and addMissing make some markers misclassified or missing at random

References

• J B S Haldane (1930) Theoretical genetics of autopolyploids. Journal of genetics 22 359--372

• Ripol, M I et al(1999) Statistical aspects of genetic mapping in autopolyploids. Gene 235 31--41

Examples

# NOT RUN {
## expected segregation proportions heterogeneous parents
expected.segRatio(4)
expected.segRatio("Tetraploid")
expected.segRatio("Octa")

## expected segregation proportions homogeneous parents
expected.segRatio("Octa",type="heter")

## generate dominant markers for autotetraploids
a1 <- sim.autoMarkers(4,c(0.8,0.2))
print(a1)
plot(a1)

## generate crosses for different parental types
p2 <- sim.autoCross(4, dose.proportion=list(p01=c(0.7,0.3),
                     p10=c(0.7,0.3),p11=c(0.6,0.2,0.2)))
print(p2)
plot(p2)

## simulate and test some markers, printing out a summary table of
## no.s of correct marker dosages 

a <- sim.autoMarkers(ploidy = 8, c(0.7,0.2,0.09,0.01),
                     type="hetero", n.markers=500,n.individuals=100)
a <- addMissing(a, 0.07)  # make seven percent missing at random
at <- test.segRatio(a$seg.ratios, ploidy=8, type.parents="het",
                      method="bin")
print(addmargins(table(a$true.doses$dosage, at$dosage, exclude=NULL)))

# }