check: Check consistency of data in pedigree
In GeneticsPed: Pedigree and genetic relationship functions

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	check(x, ...) checkId(x)

`x`	pedigree, object to be checked
`...`	arguments to other methods, none for now

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.

List of more or less self-explanatory errors and "pointers" to these errors for ease of further work i.e. removing errors.

Gregor Gorjanc

Pedigree

  ## 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)

Loading required package: MASS

Attaching package: ‘GeneticsPed’

The following object is masked from ‘package:stats’:

    family

   id father mother generation sex
1   1     NA     NA          1   1
2   2     NA     NA          1   1
3   3     NA     NA          1   2
4   4     NA     NA          1   2
5   5     NA     NA          1   2
6   6      2      4          2   1
7   7      2      5          2   1
8   8      2      3          2   2
9   9      2      5          2   2
10 10      1      5          2   2
11 11      7      8          3   2
12 12      7     10          3   2
13 13      6     10          3   1
14 14      6      8          3   2
15 15      7      9          3   2
   id father mother generation sex
1   1     NA     NA          1   1
2   2     NA     NA          1   1
3   3     NA     NA          1   2
4   4     NA     NA          1   2
5   5     NA     NA          1   2
6   6      2      4          2   1
7   7      2      5          2   1
8   8      2      3          2   2
9   9      2      5          2   2
10 10      1      5          2   2
11 11      7      8          3   2
12 12      7     10          3   2
13 13      6     10          3   1
14 14      6      8          3   2
15 15      7      9          3   2
[1] "factor"
[1] "integer"
Error in GeneticsPed:::idClass(tmp) : 
  columns ‘id’, ‘father’, ‘mother’ must have the same class
$idIsNA
$idIsNA$message
[1] "‘id’ id can not be NA"

$idIsNA$rowIndex
[1] 1


$idNotUnique
$idNotUnique$message
[1] "‘id’ must be unique"

$idNotUnique$rowIndex
[1] 1 2


[1] 0
$fatherEqualsmother
$fatherEqualsmother$message
[1] "‘father’ id can not be equal to id of ‘mother’"

$fatherEqualsmother$rowIndex
[1] 3


$fatherInmother
$fatherInmother$message
[1] "‘father’ id can not be in id of ‘mother’"

$fatherInmother$rowIndex
[1] 3


$`father1|father2Inmother`
$`father1|father2Inmother`$message
[1] "‘father1|father2’ id can not be in id of ‘mother’"

$`father1|father2Inmother`$rowIndex
[1] 1 2 3 4


$unusedLevelsInfather
$unusedLevelsInfather$message
[1] "unused levels in ‘father’"

$unusedLevelsInfather$levels
[1] "1"