test.segRatio {polySegratio}R Documentation

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

Author(s)

Peter Baker p.baker1@uq.edu.au

References

See Also

segregationRatios for computing segregation ratios and segRatio, expected.segRatio

Examples


  ## 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)))

[Package polySegratio version 0.2-3 Index]