calc_homologprob: Homolog probabilities

In mmollina/MAPpoly: Genetic Linkage Maps in Autopolyploids

Homolog probabilities

Description

Compute homolog probabilities for all individuals in the full-sib population given a map and conditional genotype probabilities.

Usage

calc_homologprob(input.genoprobs, verbose = TRUE)

Arguments

input.genoprobs	an object of class mappoly.genoprob
verbose	if TRUE (default), the current progress is shown; if FALSE, no output is produced

Author(s)

Marcelo Mollinari, [e-mail]

References

Mollinari M., Olukolu B. A., Pereira G. da S., Khan A., Gemenet D., Yencho G. C., Zeng Z-B. (2020), Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping, _G3: Genes, Genomes, Genetics_. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400620")}

Examples

   
     ## tetraploid example
     w1 <- calc_genoprob(solcap.dose.map[[1]])
     h.prob <- calc_homologprob(w1)
     print(h.prob)
     plot(h.prob, ind = 5, use.plotly = FALSE)
     ## using error modeling (removing noise)
     w2 <- calc_genoprob_error(solcap.err.map[[1]])
     h.prob2 <- calc_homologprob(w2)
     print(h.prob2)
     plot(h.prob2, ind = 5, use.plotly = FALSE)
  

mmollina/MAPpoly documentation built on March 9, 2024, 2:52 a.m.