impute_parent: 'Impute Parent Genotype'

In yangjl/imputeR: Imputation of GBS genotypes via window phasing

Description

We have observed parent and observed kids. We want to know the likelihood of the parent's possible genotypes. This function is to impute the parent's most likely genotype from a progeny array of k kids by giving a log likelihood threshold.

Usage

impute_parent(GBS.array, perr, kerr)

impute_one_site(locus, gen_error, p_locus, probs, parents, obs_parent,
  other_parents, obs_kids, true_p)

parentgeno(geno, oddratio = 0.69, returnall = TRUE)

Arguments

GBS.array	A GBS.array object generated from create_array() or sim.array() functions. In the object, a vector (at slot freq) of allele frequencies for each locus will be provided. It was estimated from the selfed progeny.
parents	A list of the genotypes of all possible parents, including current parent. These are observed GBS data, coded with 0, 1 and 2, which is the copy of alternative alleles. Missing data should be coded with 3.
obs_parent	An integer referring to which parent is the current parent of interest.
other_parents	A vector of integers referring to which are the second parent of each kid. Should be same length as number of kids (length(obs_kids))
obs_kids	A list of vectors of Kid's GBS data. Coded with 0, 1 and 2, which is the copy of alternative alleles. Missing data should be coded with 3.
geno	A table of genotype likelihoods from impute_parent
oddratio	The cutoff used for determining the log likelihood ratio of the highest and the 2nd highest genotypes. The oddratio = NULL means to report the most likely genotype. Default value sets to 0.6931472, which is equivalent to most likely genotype being twice as likely as next most likely. 2X as likely
returnall	For function 'parentgeno', returnall=TRUE will return with all the information; returnall=FALSE will return parent's genotype only (either maxlikelihood or, if oddratio is specified, genotypes with low oddratios will be set to missing).
hom.error	Homozygous error rate, default=0.02.
het.error	Heterozygous error rate, default=0.8.
oddratio	The cutoff used for determining the log likelihood ratio of the highest and the 2nd highest genotypes. The oddratio = NULL means to report the most likely genotype. Default value sets to 0.6931472, which is equivalent to most likely genotype being twice as likely as next most likely. 2X as likely
returnall	If TRUE this will return all the data. Otherwise it will return the genotypes that pass the specified oddratio; if no oddratio is specied (oddratio=NULL) then this returns the maximum likelihood genotypes

Value

return a data.frame with all the log likelihoods. Using function parentgeno to extract parent's genotype.

See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more a simulated example and more details

Examples

test <- sim.array(size.array=50, numloci=10)
res <- impute_parent(GBS.array=test)
out <- parentgeno(res, oddratio=0.69, returnall=TRUE)

yangjl/imputeR documentation built on May 4, 2019, 2:28 p.m.