check: Check consistency of data in pedigree

Description

check performs a series of checks on pedigree object to ensure consistency of data.

Usage

check(x, ...)
checkId(x)

Arguments

pedigree, object to be checked

...

arguments to other methods, none for now

Value

these errors for ease of further work i.e. removing errors.

Details

checkId performs various checks on individuals and their ascendants. These checks are:

idClass: all ids must have the same class
idIsNA: individual can not be NA
idNotUnique: individual must be unique
idEqualAscendant: individual can not be equal to its ascendant
ascendantEqualAscendant: ascendant can not be equal to another ascendant
ascendantInAscendant: ascendant can not appear again as asescendant of other sex i.e. father can not be a mother to someone else
unusedLevels: in case factors are used for id presentation, there might be unused levels for some ids - some functions rely on number of levels and a check is provided for this

checkAttributes is intended primarly for internal use and performs a series of checks on attribute values needed in various functions. It causes stop with error messages for all given attribute checks.

Examples

Run this code

  ## EXAMPLES BELLOW ARE ONLY FOR TESTING PURPOSES AND ARE NOT INTENDED
  ## FOR USERS, BUT IT CAN NOT DO ANY HARM.

  ## --- checkAttributes ---
  tmp <- generatePedigree(5)
  attr(tmp, "sorted") <- FALSE
  attr(tmp, "coded") <- FALSE
  GeneticsPed:::checkAttributes(tmp)
  try(GeneticsPed:::checkAttributes(tmp, sorted=TRUE, coded=TRUE))

  ## --- idClass ---
  tmp <- generatePedigree(5)
  tmp$id <- factor(tmp$id)
  class(tmp$id)
  class(tmp$father)
  try(GeneticsPed:::idClass(tmp))

  ## --- idIsNA ---
  tmp <- generatePedigree(2)
  tmp[1, 1] <- NA
  GeneticsPed:::idIsNA(tmp)

  ## --- idNotUnique ---
  tmp <- generatePedigree(2)
  tmp[2, 1] <- 1
  GeneticsPed:::idNotUnique(tmp)

  ## --- idEqualAscendant ---
  tmp <- generatePedigree(2)
  tmp[3, 2] <- tmp[3, 1]
  GeneticsPed:::idEqualAscendant(tmp)

  ## --- ascendantEqualAscendant ---
  tmp <- generatePedigree(2)
  tmp[3, 2] <- tmp[3, 3]
  GeneticsPed:::ascendantEqualAscendant(tmp)

  ## --- ascendantInAscendant ---
  tmp <- generatePedigree(2)
  tmp[3, 2] <- tmp[5, 3]
  GeneticsPed:::ascendantInAscendant(tmp)
  ## Example with multiple parents
  tmp <- data.frame(id=c("A", "B", "C", "D"),
                    father1=c("E", NA, "F", "H"),
                    father2=c("F", "E", "E", "I"),
                    mother=c("G", NA, "H", "E"))
  tmp <- Pedigree(tmp, ascendant=c("father1", "father2", "mother"),
                  ascendantSex=c(1, 1, 2),
                  ascendantLevel=c(1, 1, 1))
  GeneticsPed:::ascendantInAscendant(tmp)

  ## --- unusedLevels ---
  tmp <- generatePedigree(2, colClass="factor")
  tmp[3:4, 2] <- NA
  GeneticsPed:::unusedLevels(tmp)