process_inputs {qtl2pleio}

Process inputs to scan functions

Description

Process inputs to scan functions

Usage

process_inputs(
  probs,
  pheno,
  addcovar,
  kinship,
  n_snp = dim(probs)[3],
  start_snp = 1,
  max_iter = 10^4,
  max_prec = 1/10^8
)

Arguments

probs

a three-dimensional array of founder allele probabilities

pheno

a matrix of d trait values

addcovar

a matrix of covariates

kinship

a kinship matrix

n_snp

number of markers

start_snp

index number of start position in the probs object.

max_iter

max number of iterations for EM

max_prec

max precision for stopping EM