test.segRatio function

Classic tests for assessing marker dosage in autopolyploids

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

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

Returns

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

Author(s)

Peter Baker p.baker1@uq.edu.au

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)))