onemap (version 3.0.0)

create_probs: Build genotype probabilities matrix for hmm

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(
  input.obj = NULL,
  global_error = NULL,
  genotypes_errors = NULL,
  genotypes_probs = NULL
)

Value

An object of class onemap, i.e., a list with the following components:

geno

a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.

n.ind

number of individuals.

n.mar

number of markers.

segr.type

a vector with the segregation type of each marker, as strings.

segr.type.num

a vector with the segregation type of each marker, represented in a simplified manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corresponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6 corresponds to markers of type "D1" and 7 corresponds to markers of type "D2". Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.

input

the name of the input file.

n.phe

number of phenotypes.

pheno

a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.

error

matrix containing HMM emission probabilities

Arguments

input.obj

object of class onemap or onemap sequence

global_error

a integer specifying the global error value

genotypes_errors

a matrix with dimensions (number of individuals) 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).

Author

Cristiane Taniguti

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.

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, global_error = 10^-5)