mpimpute: Impute missing values for an mpcross object

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Use multi-point founder probabilities to fill in the most likely value for a missing genotype

Usage

mpimpute(object, what = c("both", "founders", "finals"), threshold = 0.5,
  calls = c("discrete", "continuous"), ...)

Arguments

object	Object of class mpcross
what	Whether to impute founders, finals, or both
threshold	Threshold for probability to call an allele
calls	Form of the finals output - discrete (genotype calls if above the threshold), or continuous (expectation of allele). For multiallelic markers no value will be imputed if continuous output is selected.
...	Additional parameters to be passed into mpprob function

Value

An mpcross object with a new component $missfinals and $missfounders for the original set of genotypes. The components $finals and $founders replaced by the imputed values.

References

Huang BE, Raghavan C, Mauleon R, Broman KW, Leung H (under review) Imputation of low-coverage genotyping-by-sequencing in multi-parental crosses.

See Also

mpprob, mpcross

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.