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.
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"
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).
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
)
#> ClusterIndex id father mother sex
#> 1 1 M2AM8 <NA> <NA> 1
#> 2 1 M273P <NA> <NA> 2
#> 3 1 M20AM <NA> <NA> 1
#> 4 1 M28TU <NA> <NA> 2
#> 5 1 M228J <NA> <NA> 1
#> 6 1 M200F <NA> <NA> 2
#> 7 1 M10XC M228J M200F 1
#> 8 1 M1YP0 M228J M200F 2
#> 9 1 M220J M228J M200F 1
#> 10 1 M22AM M228J M200F 1
#> 11 1 M2772 M228J M200F 1
#> 12 1 M28LU M228J M200F 2
#> 13 1 M2AXE M228J M200F 2
#> 14 1 M2C1T M228J M200F 2
#> 15 1 MSV10T MSV00E M28LU 2
#> 16 1 MSV1C0 MSV00E M28LU 1
#> 17 1 MSV1EX MSV00E M28LU 1
#> 18 1 MSV1F5 MSV00E M28LU 1
#> 19 1 MSV1F8 MSV00E M28LU 2
#> 20 1 MSV1FJ MSV00E M28LU 1
#> 21 1 MSV1FL MSV00E M28LU 1
#> 22 1 MSV1FT MSV00E M28LU 1
#> 23 1 MSV1TM MSV00E M28LU 2
#> 24 1 MSV01X M2772 M28TU 1
#> 25 1 MSV055 M2772 M28TU 2
#> 26 1 MSV0AL M2772 M28TU 1
#> 27 1 MSV0TA M2772 M28TU 1
#> 28 1 MSV0XT M2772 M28TU 1
#> 29 1 MSV17U M2772 M28TU 1
#> 30 1 MSV180 M2772 M28TU 2
#> 31 1 MSV18C M2772 M28TU 2
#> 32 1 MSV1KT M2772 M28TU 2
#> 33 1 M1J47 M2AM8 M200F 1
#> 34 1 M221C M2AM8 M200F 2
#> 35 1 M2C8Y M2AM8 M200F 2
#> 36 1 M2F1L M2AM8 M200F 2
#> 37 1 MSV02F M2AM8 M200F 1
#> 38 1 MSV02L M2AM8 M200F 1
#> 39 1 MSV0CK M2AM8 M200F 2
#> 40 1 MSV0FK M2AM8 M200F 1
#> 41 1 MSV0H5 M2AM8 M200F 2
#> 42 1 MSV0P7 M2AM8 M200F 1
#> 43 1 MSV0UP M2AM8 M200F 2
#> 44 1 MSV0UT M2AM8 M200F 1
#> 45 1 MSV0UU M2AM8 M200F 2
#> 46 1 MSV16T M2AM8 M200F 2
#> 47 1 MSV16U M2AM8 M200F 1
#> 48 1 MSV170 M2AM8 M200F 1
#> 49 1 MSV177 M2AM8 M200F 2
#> 50 1 MSV1FE M2AM8 M200F 1
#> 51 1 M2757 M20AM M273P 2
#> 52 1 M2ALK M20AM M273P 2
#> 53 1 M2ETE M20AM M273P 2
#> 54 1 M2EUJ M20AM M273P 2
#> 55 1 MSV00E M20AM M273P 1
#> 56 1 MSV018 M20AM M273P 1
#> 57 1 MSV05L M20AM M273P 1
#> 58 1 MSV0M6 M20AM M273P 1
#> 59 1 MSV0T4 M20AM M273P 1
#> 60 1 MSV0T7 M20AM M273P 1
#> 61 1 MSV0TJ M20AM M273P 2
#> 62 1 MSV0UL M20AM M273P 1
#> 63 1 MSV0X4 M20AM M273P 1
#> 64 1 MSV17F M20AM M273P 2
#> 65 1 MSV1MH M20AM M273P 2