polyRAD_genotype: OneMap interface with polyRAD package
In Cristianetaniguti/genotyping4onemap: genotyping4onemap

Description Usage Arguments Value Author(s) References See Also

View source: R/polyRAD_genotype.R

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

polyRAD_genotype(
  vcf = NULL,
  onemap.obj = NULL,
  parent1 = NULL,
  parent2 = NULL,
  f1 = NULL,
  crosstype = NULL,
  global_error = NULL,
  use_genotypes_errors = TRUE,
  use_genotypes_probs = FALSE,
  rm_multiallelic = TRUE
)

`vcf`	path to vcf file
`onemap.obj`	object of onemap class
`parent1`	parent 1 identification in vcfR object
`parent2`	parent 2 identification in vcfR objetc
`f1`	f1 individual identification if F2 cross type
`crosstype`	string defining the cross type, by now it supports only outcross and f2 intercross
`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

onemap object with genotypes updated

Cristiane Taniguti, chtaniguti@usp.br

Clark LV, Lipka AE, and Sacks EJ (2019) Improvements to Genotype Calling in Polyploids Using the polyRAD R Package. Plant and Animal Genome Conference XXVII, January 12-16, San Diego, California, USA. doi:10.13140/RG.2.2.18358.75847

Clark LV, Lipka AE, and Sacks EJ (2018) polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. Plant and Animal Genome Conference XXVI, January 13-17, San Diego, California, USA. doi:10.13140/RG.2.2.27134.08001

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

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