polySegratio (version 0.2-5)

test.segRatio: Classic tests for assessing marker dosage in autopolyploids

Description

Perform chi--squared tests or binomial CIs to obtain expected marker dosage in autopolyploids

Usage

test.segRatio(seg.ratio, ploidy.level = 4,
  type.parents = c("heterogeneous", "homozygous"),
  method = c("chi.squared", "binomial"), alpha = 0.05, expected.ratio)

Arguments

seg.ratio

object of class segRatio containing segregation proportions

ploidy.level

the number of homologous chromosomes, either as numeric or as a character string

type.parents

"heterogeneous" if parental markers are 0,1 or "homozygous" if parental markers are both 1

method

specify which method ‘chi.squared’ or ‘binomial’

alpha

significance level for tests/CIs

expected.ratio

vector of expected segregation proportions Default: determined by using function expected.segRatio given the ploidy.level

Value

Returns object of class testSegRatio with components

probability

matrix of probabilities under the test for each dosage where columns are doses and rows are markers

dosage

vector of allocated dosages where allocation unique otherwise NA

allocated

matrix of 0's and 1's where 1 indicates dosage allocation where columns are doses and rows are markers

alpha

alpha level for significance test or CI construction

expected.ratios

expected segregation ratios under null hypotheses

call

call to test.segRatio

References

• K Mather(1951) The measurement of linkage in heredity. Methuen London

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

See Also

segregationRatios for computing segregation ratios and segRatio, expected.segRatio

Examples

# NOT RUN {
  ## simulated data
  a <- sim.autoMarkers(ploidy = 8, c(0.7,0.2,0.09,0.01))
  print(a)

  ## summarise chi-squared test vs true
  ac <- test.segRatio(a$seg.ratios, ploidy=8, method="chi.squared")
  print(addmargins(table(a$true.doses$dosage, ac$dosage, exclude=NULL)))

  ## summarise binomial CI vs true
  ab <- test.segRatio(a$seg.ratios, ploidy=8, method="bin")
  print(addmargins(table(a$true.doses$dosage, ab$dosage, exclude=NULL)))
# }