Check the a GSP (in prepped list format) for inbreeding loops — check_pedigree_for

After a GSP has been passed through prep_gsp_for_hap_dropping() it is in a list format with the individuals ordered in such a way that it should be easy to check for any inbreeding loops in it (which are not allowed!). This version uses a simple recursive approach to compute the ancestry vector for each individual, and it detects inbreeding by the occurrence of the same ID in the ancestry vector more than once. This might be slow on large pedigrees, but for most that people would use, this should be fine.

check_pedigree_for_inbreeding(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. It throws an error via stop() if inbreeeding loops are found in the pedigree. Before throwing that error it lists the individuals with repeated occurrences in their ancestry vectors via the message() function.

Details

Note that the ancestry vector produced by this is not ordered the way the ancestry vectors are in my package CKMRpop---for simplicity I just get a list of ancestors in whatever order they happen to be reached.

Examples

# get the 13 member pedigree in the data object GSP and
# turn it into a list
GP <- prep_gsp_for_hap_dropping(GSP)

# check it for inbreeding. (There is none)
check_pedigree_for_inbreeding(GP)

## This one will fail, so we wrap it in tryCatch so CRAN
## check doesn't find it a problem.
# To see what happens if there are inbreeding loops, make some
GP_inbred <-  GP
# make 12 be inbred trough individual 6
GP_inbred$`12`$par1$par = "13"
# make 8 inbred (because both of its founder parents are the same!)
GP_inbred$`8`$par2$par = "4"

# now try that:
tryCatch(
  check_pedigree_for_inbreeding(GP_inbred),
  error = function(x) 0,
  warning = function(x) 0
)
#> ID 8 in the GSP has the same individual(s) more than once in its ancestry: 4
#> ID 10 in the GSP has the same individual(s) more than once in its ancestry: 4
#> ID 11 in the GSP has the same individual(s) more than once in its ancestry: 4
#> ID 12 in the GSP has the same individual(s) more than once in its ancestry: 4, 6
#> Such duplicated IDs imply a pedigree with inbreeding.  Not allowed.
#> [1] 0