create_probs: Build genotype probabilities matrix for hmm

In Cristianetaniguti/genotyping4onemap: genotyping4onemap

Description

The genotypes probabilities can be calculated considering a global error (default method) or considering a genotype error probability for each genotype. Furthermore, user can provide directly the genotype probability matrix.

Usage

create_probs(
  onemap.obj = NULL,
  global_error = NULL,
  genotypes_errors = NULL,
  genotypes_probs = NULL
)

Arguments

onemap.obj	an object of class onemap.
global_error	a integer specifing the global error value
genotypes_errors	a matrix with dimensions (number of marker) x (number of markers) with genotypes errors values
genotypes_probs	a matrix with dimensions (number of individuals)*(number of markers) x possible genotypes (i.e., a ab ba b) with four columns for f2 and outcrossing populations, and two for backcross and RILs).

Details

The genotype probability matrix has number of individuals x number of markers rows and four columns (or two if considering backcross or RILs populations), one for each possible genotype of the population. This format follows the one proposed by MAPpoly.

The genotype probabilities come from SNP calling methods. If you do not have them, you can use a global error or a error value for each genotype. The OneMap until 2.1 version have only the global error option.

Value

An object of class onemap with the built matrix at prob component of the list

Author(s)

Cristiane Taniguti [e-mail]

References

Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43

See Also

make_seq

Examples

  data(onemap_example_out)
  new.data <- create_probs(onemap_example_out, prob = 10^-5)
  
  

Cristianetaniguti/genotyping4onemap documentation built on Aug. 26, 2020, 10:32 a.m.