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Normalise a Rel object dataframe

Source: R/norm_data.R
norm_rel.Rd

Normalise a dataframe and check for columns correspondance to be able to use it as an input to create a Ped object.

Usage

norm_rel(rel_df, na_strings = c("NA", ""), missid = NA_character_)

Arguments

rel_df

A data.frame with the special relationships between individuals. See Rel() for more informations. The minimum columns required are id1, id2 and code. The famid column can also be used to specify the family of the individuals. If a matrix is given, the columns needs to be ordered as id1, id2, code and famid. The code values are:

  • 1 = Monozygotic twin

  • 2 = Dizygotic twin

  • 3 = twin of unknown zygosity

  • 4 = Spouse

The value relation code recognized by the function are the one defined by the rel_code_to_factor() function.

na_strings

Vector of strings to be considered as NA values.

missid

A character vector with the missing values identifiers. All the id, dadid and momid corresponding to those values will be set to NA_character_.

Value

A dataframe with the errors identified

Details

The famid column, if provided, will be merged to the ids field separated by an underscore using the upd_famid() function. The code column will be transformed with the rel_code_to_factor(). Multiple test are done and errors are checked.

A number of checks are done to ensure the dataframe is correct:

On identifiers:

  • All ids (id1, id2) are not empty (!= "")

  • id1 and id2 are not the same

On code

  • All code are recognised as either "MZ twin", "DZ twin", "UZ twin" or "Spouse"

Examples

df <- data.frame(
    id1 = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
    id2 = c(2, 3, 4, 5, 6, 7, 8, 9, 10, 1),
    code = c("MZ twin", "DZ twin", "UZ twin", "Spouse",
        1, 2, 3, 4, "MzTwin", "sp oUse"),
    famid = c(1, 1, 1, 1, 1, 1, 1, 2, 2, 2)
)
norm_rel(df)
#>     id1  id2    code famid error
#> 1   1_1  1_2 MZ twin     1  <NA>
#> 2   1_2  1_3 DZ twin     1  <NA>
#> 3   1_3  1_4 UZ twin     1  <NA>
#> 4   1_4  1_5  Spouse     1  <NA>
#> 5   1_5  1_6 MZ twin     1  <NA>
#> 6   1_6  1_7 DZ twin     1  <NA>
#> 7   1_7  1_8 UZ twin     1  <NA>
#> 8   2_8  2_9  Spouse     2  <NA>
#> 9   2_9 2_10 MZ twin     2  <NA>
#> 10 2_10  2_1  Spouse     2  <NA>