Create a GSP from user inputs about what type of hybrids from which populations to create hybrids

Source: R/create_GSP.R

This function allows the user to choose two populations and create a GSP input for 'gscramble'. The input requires two different population IDs of class character as well as at least one TRUE statement for one of the hybrid parameters (F1, F2, F1B, F1B2). The GSP will indicate hybrid individuals that will be sampled based on which F1, F2, F1B, and F1B2 parameters are TRUE. F1= TRUE means F1 hybrids will be sampled. F2=TRUE means F2 hybrids will be sampled. F1B2=TRUE means F1 backcross hybrids will be sampled. F1B2=TRUE means F1 backcross 2 hybrids will be sampled. Default setting for these parameters is FALSE. The function then outputs a GSP in tibble format that can be used for other functions in 'gscramble' including check_pedigree_for_inbreeding() and prep_gsp_for_hap_dropping().

create_GSP(
  pop1,
  pop2,
  F1 = FALSE,
  F2 = FALSE,
  F1B = FALSE,
  F1B2 = FALSE,
  AllowSinglePop = FALSE
)

Arguments

pop1

character name for population 1

pop2

character name for population 2

F1

logical indicating whether you would like to have sampled F1 hybrids in the output.

F2

logical indicating whether you would like to have sampled F2 hybrids in the output.

F1B

logical indicating whether you would like to have sampled F1 backcross hybrids in the output.

F1B2

logical indicating whether you would like to have sampled F1 backcross 2 hybrids in the output.

AllowSinglePop

Set to true if you want all the founders from just a single population. This has some use cases...

Value

This function returns a GSP in tibble format with the user argument for pop1 and pop2 autopopulated in the hpop1 and hpop2 columns.

Examples

# create a GSP that generates hybrids and samples F1s and F1B's from pops A and B
gsp <- create_GSP("A", "B", F1 = TRUE, F1B = TRUE)

#create a GSP that generates hybrids and samples F1s, F2s, F1Bs, F1B2s from pops A and B
gsp <- create_GSP("Pop_X", "Pop_Z", F1 = TRUE, F2 = TRUE, F1B = TRUE, F1B2 = TRUE)