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Find all rows which are part of a set of duplicated rows

flag_duplicates.Rd

Many duplication tools such as base::duplicated() or dplyr::distinct() identify rows which are duplications. It is often useful to see ALL rows which are part of the duplication set, and not just the second row.

creates new column: dup_rsid or dup_chr_pos, a T/F flag. Specifically, flags both rows in a duplication pair, and not just first or last duplicate row, making it easy to work with all rows that are part of a duplication

Usage

flag_duplicates(
  tbl,
  column = c("rsid", "chr_pos", "chr_pos_ref_alt", "rsid_ref_alt")
)

Arguments

tbl

a dplyr::tibble()

column

Which columns should be used to form a unique ID?

Value

a tibble with a new column marking duplicates

Examples

if (FALSE) { # \dontrun{

# will tag multi-allelics as duplications
flag_duplicates(tbl, column = "rsid")
flag_duplicates(tbl, column = "chr_pos")
# if you are interested in rows that are variant duplications
flag_duplicates(tbl, column = "rsid_ref_alt")
flag_duplicates(tbl, column = "chr_pos_ref_alt")

} # }