check_gsp_for_validity_and_saturation {gscramble}

Check that GSP does not reuse genetic material and yet uses all of it

Description

These conditions can be checked for a GSP with no inbreeding loops simply by ensuring that the amount of genetic material coming into each individual is the same as the amount going out (either as segregated gametes or as samples). If the amount of material coming out of any individual in the GSP is greater than the amount coming in, then an error is thrown. If the amount coming out is less than the amount coming in, then a warning about the GSP is thrown. Messages printed via message() and warning() indicate which individuals in the GSP are problematic. All problematic individuals are listed before an error is thrown with stop().

Usage

check_gsp_for_validity_and_saturation(GP)

Arguments

GP

A gsp in list format as produced by the function prep_gsp_for_hap_dropping(). See the documentation for the return object of prep_gsp_for_hap_dropping() for a description.

Value

This function does not return anything.

Examples

# get the 13 member pedigree in tibble form as the package
# and turn it into a list
GP <- prep_gsp_for_hap_dropping(GSP)

# check it. (This passes)
check_gsp_for_validity_and_saturation(GP)

## The following will show a failure, so we wrap it in tryCatch
## so CRAN check does not flag it as a problem.
# Read in a gsp with errors and then make sure all the
# error in it are caught
bad <- readr::read_csv(system.file("extdata/13-member-ped-with-errors.csv", package = "gscramble"))

# check_gsp_for_validity_and_saturation() is called internally from
# within prep_gsp_for_hap_dropping(), after creating a list-from GSP.
# This will show the error produced by check_gsp_for_validity_and_saturation().
badL <- tryCatch(
  prep_gsp_for_hap_dropping(bad),
  error = function(x) 0,
  warning = function(x) 0
)