plot_progeny_dosage_change: Display genotypes imputed or changed by the HMM chain given a...

In mappoly: Genetic Linkage Maps in Autopolyploids

Display genotypes imputed or changed by the HMM chain given a global genotypic error

Description

Outputs a graphical representation ggplot with the percent of data changed.

Usage

plot_progeny_dosage_change(
  map_list,
  error,
  verbose = TRUE,
  output_corrected = FALSE
)

Arguments

map_list	a list of multiple mappoly.map.list
error	error rate used in global error in the 'calc_genoprob_error()'
verbose	if TRUE (default), current progress is shown; if FALSE, no output is produced
output_corrected	logical. if FALSE only the ggplot of the changed dosage is printed, if TRUE then a new corrected dosage matrix is output.

Value

A ggplot of the changed and imputed genotypic dosages

Author(s)

Jeekin Lau, [e-mail], with optimization by Cristiane Taniguti, [e-mail]

Examples

      x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE)   
      plot_progeny_dosage_change(list(x), error=0.05, output_corrected=FALSE) 
      corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, 
      output_corrected=FALSE) #output corrected

mappoly documentation built on May 29, 2024, 6:05 a.m.