calc_genoprob: Calculate conditional genotype probabilities

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Calculate conditional genotype probabilities

Description

Uses a hidden Markov model to calculate the probabilities of the true underlying genotypes given the observed multipoint marker data, with possible allowance for genotyping errors.

Usage

calc_genoprob(
  cross,
  map = NULL,
  error_prob = 0.0001,
  map_function = c("haldane", "kosambi", "c-f", "morgan"),
  lowmem = FALSE,
  quiet = TRUE,
  cores = 1
)

Arguments

cross	Object of class "cross2". For details, see the R/qtl2 developer guide.
map	Genetic map of markers. May include pseudomarker locations (that is, locations that are not within the marker genotype data). If NULL, the genetic map in cross is used.
error_prob	Assumed genotyping error probability
map_function	Character string indicating the map function to use to convert genetic distances to recombination fractions.
lowmem	If FALSE, split individuals into groups with common sex and crossinfo and then precalculate the transition matrices for a chromosome; potentially a lot faster but using more memory.
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().

Details

Let O_k denote the observed marker genotype at position k, and g_k denote the corresponding true underlying genotype.

We use the forward-backward equations to calculate \alpha_{kv} = \log Pr(O_1, \ldots, O_k, g_k = v) and \beta_{kv} = \log Pr(O_{k+1}, \ldots, O_n | g_k = v)

We then obtain Pr(g_k | O_1, \ldots, O_n) = \exp(\alpha_{kv} + \beta_{kv}) / s where s = \sum_v \exp(\alpha_{kv} + \beta_{kv})

Value

An object of class "calc_genoprob": a list of three-dimensional arrays of probabilities, individuals x genotypes x positions. (Note that the arrangement is different from R/qtl.) Also contains four 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.

• alleleprobs - Logical value (FALSE) that indicates whether the probabilities are compressed to allele probabilities, as from genoprob_to_alleleprob().

See Also

insert_pseudomarkers()

Examples

grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, gmap_w_pmar, error_prob=0.002)

qtl2 documentation built on June 8, 2025, 10:25 a.m.