probs_doqtl_to_qtl2 {qtl2convert}

Convert DOQTL genotype probabilities to R/qtl2 format

Description

Convert DOQTL genotype probabilities to R/qtl2 format

Usage

probs_doqtl_to_qtl2(
  probs,
  map,
  is_female = NULL,
  chr_column = "chr",
  pos_column = "cM",
  marker_column = "marker"
)

Arguments

probs

3d array of genotype probabilities as calculated from DOQTL (individuals x genotypes x positions)

map

Data frame with marker map

is_female

Optional logical vector indicating which individuals are female. Names should contain the individual identifiers, matching the row names in probs.

chr_column

Name of the column in map that contains the chromosome IDs.

pos_column

Name of the column in map that contains the marker positions.

marker_column

Name of the column in map that contains the marker names. If NULL, use the row names.

Details

We assume that the X chromosome is labeled "X" (must be upper-case) and that any other chromosomes are autosomes. We assume that the genotypes are labeled using the 8 letters A-H.

If the probabilities are for the full 36 states and the X chromosome is included but is_female is not provided, we'll guess which individuals are females based on their genotype probabilities. (If the average, across loci, of the sum of the heterozygote probabilities is small, we'll assume it's a female.)

Value

An object of the form produced by qtl2::calc_genoprob().