probs_qtl2_to_doqtl {qtl2convert}

Convert R/qtl2 genotype probabilities to DOQTL format

Description

Convert R/qtl2 genotype probabilities to DOQTL format

Usage

probs_qtl2_to_doqtl(probs)

Arguments

probs

A "calc_genoprob" object (a list of 3d arrays of genotype probabilities), as calculated by qtl2::calc_genoprob().

Details

If the arrays in probs all have 8 columns, they're assumed to be allele dosages and we paste them all together into one big array.

Otherwise, it should be that the autosomes all have 36 columns the X chromosome has 44. In this case, the male hemizygotes on the X are placed where the female homozygotes are, and then we reorder the genotypes into alphabetical order.

Value

A single three-dimensional array, for use with DOQTL.