R/create.genotype.states.R

In DOQTL: Genotyping and QTL Mapping in DO Mice

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# Given a set of founders, create all of the possible unphased genotype states 
# between them.
# Daniel Gatti
# Dan.Gatti@jax.org
# June 7, 2013
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# Arguments: founders, character vector with founder letters.
#            sampletype: one of "DO, "HS", "CC", or "HSrat"
create.genotype.states = function(founders, sampletype = c("DO", "CC", "HS", "HSrat")) {
  sampletype = match.arg(sampletype)
  states = NULL
  if(sampletype == "CC") {
    states = paste0(founders, founders)
  } else {
    states = outer(founders, founders, paste, sep = "")
    states = sort(states[upper.tri(states, diag = TRUE)])
  } # else
  return(list(auto = states, X = list(F = states, M = founders),
         founders = founders))
} # create.genotype.states()