process_inputs: Process inputs to scan functions
In qtl2pleio: Testing Pleiotropy in Multiparental Populations

Process inputs to scan functions

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

`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