Remove duplicate records from pedigree

Part of Pedigree Curation

Usage

removeDuplicates(ped, reportErrors = FALSE)

Arguments

ped

dataframe that is the Pedigree. It contains pedigree information. The id and recordStatus columns are required.

reportErrors

logical value if TRUE the function returns a character vector of duplicate id values (or NULL when none are found) instead of the de-duplicated pedigree. Only records whose recordStatus is "added" (the records made for parents that have no record of their own) are left out of the search; a record with any other recordStatus, including NA or a blank, is a real animal and is searched.

Value

When reportErrors is FALSE, a dataframe (the Pedigree) with duplicate rows removed; when reportErrors is TRUE, a character vector of duplicate id values, one entry for each extra occurrence of an id (or NULL when none are found).

Details

Returns an updated dataframe with duplicate rows removed.

Returns an error if the table has duplicate IDs with differing data. The error applies only when reportErrors is FALSE. Rows are compared on all columns, including recordStatus.

Examples

ped <- nprcgenekeepr::smallPed
newPed <- cbind(ped, recordStatus = rep("original", nrow(ped)))
ped1 <- removeDuplicates(newPed)
nrow(newPed)
#> [1] 17
nrow(ped1)
#> [1] 17
pedWithDups <- rbind(newPed, newPed[1:3, ])
ped2 <- removeDuplicates(pedWithDups)
nrow(pedWithDups)
#> [1] 20
nrow(ped2)
#> [1] 17