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Organizes pedigree data

Source: R/get_ped.R
get_ped.Rd

Offers an alternative to get_colony() function in cases where the pedigree was not reconstructed with COLONY software. It takes a pedigree dataframe and assigns sex to each individual. The function also prepares data so that the output of the function can be directly analyzed with kinship2, pedtools or FamAgg packages.

Usage

get_ped(ped, sampledata, out = "FamAgg")

Arguments

ped

Data frame. Pedigree data frame with the most basic structure. Three columns corresponding to offspring, father and mother (see Details). Unknown parents should be represented by NA values.

sampledata

Data frame. Metadata for all genetic samples that belong to the individuals included in pedigree reconstruction analysis. This data frame should adhere to the formatting and naming conventions outlined in the check_sampledata() documentation.

out

Character string. For use with which package should the output be formatted? kinship2 (out = "kinship2"), pedtools (out = "pedtools") or FamAgg (out = "FamAgg") or the created data.frame can be outputted as is (out = "table"). Defaults to "FamAgg"

Value

A data frame describing a common pedigree structure. Each individual included in pedigree represents one row. Columns describe individual identifier code, identifier code for mother and father and sex of individual. Column names and arrangement depends on selected output (out parameter).

Details

The custom pedigree specified through the ped parameter should mirror the structure of a COLONY pedigree and share the same column names. It should consist of three columns for each offspring: OffspringID, FatherID, MotherID. When considering unknown parents they should be represented by NA values.

Examples

#example pedigree dataframe
ped <- data.frame(
  OffspringID = c(
    "M273P", "M20AM", "M2757", "M2ALK", "M2ETE", "M2EUJ", "MSV00E",
    "MSV018", "MSV05L", "MSV0M6", "MSV0T4", "MSV0T7", "MSV0TJ", "MSV0UL"
  ),
  FatherID = c(
    NA, NA, "M20AM", "M20AM", "M20AM", "M20AM", "M20AM",
    "M20AM", "M20AM", "M20AM", "M20AM", "M20AM", "M20AM", "M20AM"
  ),
  MotherID = c(
    NA, NA, "M273P", "M273P", "M273P", "M273P", "M273P",
    "M273P", "M273P", "M273P", "M273P", "M273P", "M273P", "M273P"
  )
)
#Get pedigree data in FamAgg format
get_ped(
    ped = ped,
    sampledata = wolf_samples
    )
#>        id father mother sex
#> 1   M273P   <NA>   <NA>   2
#> 2   M20AM   <NA>   <NA>   1
#> 3   M2757  M20AM  M273P   2
#> 4   M2ALK  M20AM  M273P   2
#> 5   M2ETE  M20AM  M273P   2
#> 6   M2EUJ  M20AM  M273P   2
#> 7  MSV00E  M20AM  M273P   1
#> 8  MSV018  M20AM  M273P   1
#> 9  MSV05L  M20AM  M273P   1
#> 10 MSV0M6  M20AM  M273P   1
#> 11 MSV0T4  M20AM  M273P   1
#> 12 MSV0T7  M20AM  M273P   1
#> 13 MSV0TJ  M20AM  M273P   2
#> 14 MSV0UL  M20AM  M273P   1