updog_genotype: OneMap interface with updog package

In Cristianetaniguti/genotyping4onemap: genotyping4onemap

Description

Uses alelle counts to reestimate genotypes with updog approach and stores the genotypes probabilities or for further multipoint analysis

Usage

updog_genotype(
  vcfR.object = NULL,
  onemap.object = NULL,
  vcf.par = c("AD", "DPR"),
  parent1 = "P1",
  parent2 = "P2",
  f1 = NULL,
  recovering = FALSE,
  mean_phred = 20,
  cores = 2,
  depths = NULL,
  global_error = NULL,
  use_genotypes_errors = TRUE,
  use_genotypes_probs = FALSE,
  rm_multiallelic = TRUE
)

Arguments

vcfR.object	object output of the vcfR package
onemap.object	object of class onemap
vcf.par	Field of VCF that informs the depth of alleles
parent1	parent 1 identification in vcfR object
parent2	parent 2 identification in vcfR objetc
f1	f1 individual identification if f2 cross type
recovering	logical defining if markers should be recovered from VCF
mean_phred	the mean phred score of the sequencer technology
cores	number of threads
depths	list containing a matrix for ref and other for alt allele counts, samples ID in colum and markers ID in rows
global_error	number from 0 to 1 defining the global error to be considered together with the genotype errors or the genotype probabilities or NULL to not considered any global error
use_genotypes_errors	if TRUE the error probability of each genotype will be considered in emission function of HMM
rm_multiallelic	if TRUE multiallelic markers will be removed from the output onemap object
use_genotype_probs	if TRUE the probability of each possible genotype will be considered in emission function of HMM

Value

onemap object with genotypes updated

Author(s)

Cristiane Taniguti, [e-mail]

References

Gerard, D., Ferrão L.F.V., Garcia, A.A.F., & Stephens, M. (2018). Harnessing Empirical Bayes and Mendelian Segregation for Genotyping Autopolyploids from Messy Sequencing Data. bioRxiv. doi: 10.1101/281550.

See Also

extract_depth binom_genotype and https://github.com/dcgerard/updog.

Cristianetaniguti/genotyping4onemap documentation built on Aug. 26, 2020, 10:32 a.m.