compare_genoprob: Compare two sets of genotype probabilities
In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

compare_genoprob

R Documentation

Compare two sets of genotype probabilities

Description

Compare two sets of genotype probabilities for one individual on a single chromosome.

Usage

compare_genoprob(
  probs1,
  probs2,
  cross,
  ind = 1,
  chr = NULL,
  minprob = 0.95,
  minmarkers = 10,
  minwidth = 0,
  annotate = FALSE
)

Arguments

`probs1`	Genotype probabilities (as produced by `calc_genoprob()`) or allele dosages (as produced by `genoprob_to_alleleprob()`).
`probs2`	A second set of genotype probabilities, just like `probs1`.
`cross`	Object of class `"cross2"`. For details, see the R/qtl2 developer guide.
`ind`	Individual to plot, either a numeric index or an ID.
`chr`	Selected chromosome; a single character string.
`minprob`	Minimum probability for inferring genotypes (passed to `maxmarg()`).
`minmarkers`	Minimum number of markers in results.
`minwidth`	Minimum width in results.
`annotate`	If TRUE, add some annotations to the `geno1` and `geno2` columns to indicate, where they differ, which one matches what appears to be the best genotype. (`*` = matches the best genotype; `-` = lower match).

Details

The function does the following:

Reduce the probabilities to a set of common locations that also appear in cross.
Use maxmarg() to infer the genotype at every position using each set of probabilities.
Identify intervals where the two inferred genotypes are constant.
Within each segment, compare the observed SNP genotypes to the founders' genotypes.

Value

A data frame with each row corresponding to an interval over which probs1 and probs2 each have a fixed inferred genotype. Columns include the two inferred genotypes, the start and end points and width of the interval, and when founder genotypes are in cross, the proportions of SNPs where the individual matches each possible genotypes.

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[1,"2"]   # subset to first individual on chr 2
map <- insert_pseudomarkers(iron$gmap, step=1)

# in presence of a genotyping error, how much does error_prob matter?
iron$geno[[1]][1,3] <- 3
pr_e <- calc_genoprob(iron, map, error_prob=0.002)
pr_ne <- calc_genoprob(iron, map, error_prob=1e-15)

compare_genoprob(pr_e, pr_ne, iron, minmarkers=1, minprob=0.5)

qtl2 documentation built on May 29, 2024, 11:46 a.m.