maxmarg: Find genotypes with maximum marginal probabilities

Description

For each individual at each position, find the genotype with the maximum marginal probability.

Usage

maxmarg(
  probs,
  map = NULL,
  minprob = 0.95,
  chr = NULL,
  pos = NULL,
  return_char = FALSE,
  quiet = TRUE,
  cores = 1,
  tol = 0.0000000000001
)

Value

If chr and pos are provided, a vector of genotypes is returned. In this case, map is needed.

Otherwise, the result is a object like that returned by viterbi(), A list of two-dimensional arrays of imputed genotypes, individuals x positions. Also includes these attributes:

crosstype - The cross type of the input cross.
is_x_chr - Logical vector indicating whether chromosomes are to be treated as the X chromosome or not, from input cross.
alleles - Vector of allele codes, from input cross.

Arguments

probs: Genotype probabilities, as calculated from calc_genoprob().
map: Map of pseudomarkers in probs. Used only if chr and pos are provided.
minprob: Minimum probability for making a call. If maximum probability is less then this value, give NA.
chr: If provided (along with pos), consider only the single specified position.
pos: If provided (along with chr), consider only the single specified position.
return_char: If TRUE, return genotype names as character strings.
quiet: IF FALSE, print progress messages.
cores: Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().
tol: Tolerance value; genotypes with probability that are within tol of each other are treated as equivalent.

Details

If multiple genotypes share the maximum probability, one is chosen at random.

Examples

Run this code

# load data and calculate genotype probabilities
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
pr <- calc_genoprob(iron, error_prob=0.002)

# full set of imputed genotypes
ginf <- maxmarg(pr)

# imputed genotypes at a fixed position
g <- maxmarg(pr, iron$gmap, chr=8, pos=45.5)

# return genotype names rather than integers
g <- maxmarg(pr, iron$gmap, chr=8, pos=45.5, return_char=TRUE)