qtl2: calc_genoprob – R documentation

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calc_genoprob

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 a[k][v] = log Pr(O[1], …, O[k], g[k] = v) and b[k][v] = log Pr(O[k+1], …, O[n] | g[k] = v)

We then obtain Pr(g[k] | O[1], …, O[n] = exp(a[k][v] + b[k][v]) / s where s = sum_v exp(a[k][v] + b[k][v])

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().

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

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16