Generic function to provide starting transition probabilities. Not ready for use in this version.
Usage
generic.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", "F"))
Arguments
states
Character vector containing the genotype states coded as letters.
snps
Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
chr
Character containing the chromosome to use.
sex
Character that is either FALSE or M indicating the sex. Only used on x chromosome.
Value
A matrix of transition probabilities between genotype states.
Details
This function is a placeholder for a more sophisticated algorithm to be developed later. It is an effort to provide a set of starting transition probabilities for mapping populations other than the DO.