cr2pts: Call to the C routine for two-point analysis

Description

An interface between Rand the C routine that performs the two-point analysis. Given the type of segregation of the two markers, this function creates the corresponding vectors and matrices that are necessary to the C routine and makes a call to it.

Usage

cr2pts(mrk1, mrk2, segr.type1, segr.type2)

Arguments

mrk1

a vector containing the genotypes of all individuals for the first marker.

mrk2

a vector containing the genotypes for the second marker.

segr.type1

the type of segregation of the first marker (mrk1).

segr.type2

the type of segregation of the second marker (mrk2).

Value

Returns a list with the following components:
ra vector with the maximum likelihood estimates of the recombination fraction between both markers, under the 4 possible assignments.
likea vector with the likelihood of the data under each of the 4 assignments.
posteriora vector with the posterior probability of each of the 4 assignments.
LODa vector with the LOD Score for the 4 assignments - the base 10 logarithm of the ratio of the maximum likelihood and the likelihood under the null hypothesis of no linkage.

References

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

Examples

Run this code

data(example_out)

  # getting values
  marker1 <- example_out$geno[,1]
  marker2 <- example_out$geno[,2]
  segr.type1 <- example_out$segr.type[1]
  segr.type2 <- example_out$segr.type[2]
  
  # two-point analysis
  cr2pts(marker1,marker2,segr.type1,segr.type2)