wpeR (version 0.1.0)

get_colony: Organizes COLONY output

Description

Extends BestConfig_Ordered output from COLONY pedigree reconstruction software with additional data about individuals included in pedigree. The function adds missing parents to OffspringID, assigns sex to each individual included in OffspringID and adds the computed probabilities of paternity and maternity assignments (probability of assignments is visible only if the out parameter is set to "table"). The function also prepares data so that the output of the function can be directly analyzed with kinship2, pedtools or FamAgg packages.

Usage

get_colony(
  colony_project_path,
  sampledata,
  rm_obsolete_parents = TRUE,
  out = "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, sex and family of individual. Column names and arrangement depends on selected output (out parameter).

Arguments

colony_project_path

Character string. Path to the folder where COLONY output files are saved. Has to include file path and project name (see Details).

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.

rm_obsolete_parents

Logical. Should unknown parents be removed from output. Applies just to offspring for which both parents are unknown. Defaults to TRUE.

out

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

Details

COLONY output tables needed for this function (.BestConfig_Ordered, .Maternity and .Paternity) are read directly from the colony output folder and do not need to be imported into R session. The path to the outputs is defined with colony_project_path parameter. When defining colony_project_path the user needs to define a complete path to the directory where colony outputs are stored and also the file name (file name of COLONY outputs equals the project name
eg. /path/to/the/COLONY/output/folder/COLONY_project_name).

Examples

# Define the path to COLONY output
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")

# Get pedigree data in FamAgg format
get_colony(
    colony_project_path = path,
    sampledata = wolf_samples
    )