check_ids_match: Check ids

In Sage-Bionetworks/dccvalidator: Metadata Validation for Data Coordinating Centers

Check ids

Description

Compare IDs (such as individual IDs or specimen IDs) between two data frames.

Ensure that all individual IDs in two data frames match.

Ensure that all specimen IDS in two data frames match

Usage

check_ids_match(
  x,
  y,
  idcol = c("individualID", "specimenID"),
  xname = NULL,
  yname = NULL,
  bidirectional = TRUE
)

check_indiv_ids_match(x, y, xname = NULL, yname = NULL, bidirectional = TRUE)

check_specimen_ids_match(
  x,
  y,
  xname = NULL,
  yname = NULL,
  bidirectional = TRUE
)

Arguments

x, y	Data frames to compare
idcol	Name of column containing ids to compare
xname, yname	Names of x and y (to be used in resulting messages)
bidirectional	Should mismatches from both x and y be reported? Defaults to TRUE; if FALSE, will return only IDs in y that are not present in x (IDs in x but not y will be ignored).

Value

A condition object indicating whether IDs match ("check_pass") or not ("check_fail"). Mismatched IDs are included as data within the object.

Examples

a <- data.frame(individualID = LETTERS[1:3])
b <- data.frame(individualID = LETTERS[1:4])
check_ids_match(a, b, idcol = "individualID", xname = "a", yname = "b")
a <- data.frame(individualID = LETTERS[1:3])
b <- data.frame(individualID = LETTERS[1:4])
check_specimen_ids_match(a, b, "individual", "biospecimen")
a <- data.frame(specimenID = LETTERS[1:3])
b <- data.frame(specimenID = LETTERS[1:4])
check_specimen_ids_match(a, b, "biospecimen", "assay")

Sage-Bionetworks/dccvalidator documentation built on May 7, 2022, 10:32 a.m.