Pedigree.jl
Pedigree functions implemented in pure Julia.
NOTE: I must point out this is under contruction and none of the code is really optimized as I learn Julia. The makeA() function is still the tabular method until I can update it to make it much more efficient (either time or memory) as I go. This will happen with time, please be patient...
Please see the Wiki for more: Wiki
Summary
What it can do currently:
- Sort a pedigree with any IDs (0 is missing)
- Renumber your pedigree once sorted
- Create the A Matrix to use later or extract inbreeding values
See below for examples of each function.
The key to using my functions is to have the first 3 columns be:
- Animal
- Sire
- Dam
Each will only extract the 1st 3 columns to use, you can have any number of columns in your pedigree (such as Line, Sex, or Date of Birth), this way you don't need to subset your pedigree constantly.
What I'm implementing soon:
- Calculate A inverse directly (Henderson method, w/ and w/out inbreeding)
- Calculate the Quass L matrix (should be more memory efficient)
- Summarize the pedigree
- Check if sires are also dams and vice versa
- Check pedigree depth of each individual (see how far you can trace back ancestors)
- Look for duplicates
- Summarize family sizes
- Summarize sire and dam usage
- Hopefully parallelize parts to make it more efficient
- Integrate this package with one for genomics
Examples
Until this package gets officially registered, you have to load with Pkg.add(url="") notation (see below). Eventually you will just be able to do Pkg.add("Pedigree") after loading Pkg with using Pkg or use the package manager in REPL by clicking the ] key inside REPL.
# load Pkg package
using Pkg
# you can load the Pedigree package with:
# this package is unregistered so you have to load it like this for now
Pkg.add(url="https://github.com/austin-putz/Pedigree.jl")
# load packages
using Pedigree
using DataFrames
# generate pedigree
ped = DataFrame(
animal = ["G", "E", "K", "I", "C", "D", "L", "F", "J", "H"],
sire = ["A", "A", "H", "A", "A", "A", "A", "A", "H", "F"],
dam = ["D", "0", "I", "C", "B", "B", "J", "C", "I", "D"]
)
# notice "0" is missing!!
julia> ped
10×3 DataFrame
Row │ animal sire dam
│ String String String
─────┼────────────────────────
1 │ H F D
2 │ F A C
3 │ K H I
4 │ C A B
5 │ D A B
6 │ G A D
7 │ J H I
8 │ E A 0
9 │ I A C
10 │ L A J
stack_ancestors.jl
We can stack ancestors (parents who are not in the pedigree) on top of the pedigree with this function.
# load Pedigree package
using Pedigree
# stack ancestors
stack_ancestors(ped)
[ Info: Pedigree is a DataFrame
[ Info: Stacking 2 ancestors on top of the pedigree
12×3 DataFrame
Row │ animal sire dam
│ String String String
─────┼────────────────────────
1 │ A 0 0
2 │ B 0 0
3 │ G A D
4 │ E A 0
5 │ K H I
6 │ I A C
7 │ C A B
8 │ D A B
9 │ L A J
10 │ F A C
11 │ J H I
12 │ H F D
sort_ped.jl
This function takes a pedigree as a DataFrame (DataFrames.jl) and returns a sorted pedigree with the ancestors stacked on top (if any).
This will take any DataFrame with 1. Animal, 2. Sire, 3. Dam as a String.
using Random
# shuffle order of pedigree (to test sort_ped function)
shuffle!(ped)
# sort the pedigree
sortped = sort_ped(ped)
julia> sortped
12×3 DataFrame
Row │ animal sire dam
│ String String String
─────┼────────────────────────
1 │ A 0 0
2 │ B 0 0
3 │ C A B
4 │ F A C
5 │ D A B
6 │ H F D
7 │ I A C
8 │ J H I
9 │ K H I
10 │ G A D
11 │ E A 0
12 │ L A J
renum_ped.jl
This function is to renumber the pedigree from 1 to n and return a 3 column DataFrame as Int64.
# renumber the pedigree
renumped = renum_ped(ped)
julia> renumped
12×6 DataFrame
Row │ RenumID SireRenumID DamRenumID animal sire dam
│ Int64 Int64 Int64 String String String
─────┼──────────────────────────────────────────────────────────
1 │ 1 0 0 A 0 0
2 │ 2 0 0 B 0 0
3 │ 3 1 2 C A B
4 │ 4 1 3 F A C
5 │ 5 1 2 D A B
6 │ 6 4 5 H F D
7 │ 7 1 3 I A C
8 │ 8 6 7 J H I
9 │ 9 6 7 K H I
10 │ 10 1 5 G A D
11 │ 11 1 0 E A 0
12 │ 12 1 8 L A J
The renum_ped() function will output 6 columns, the first
3 will be the renumbered pedigree, the last 3 will be the
original IDs.
makeA.jl
Create the A matrix using the tabular method.
# create the A matrix with renumbered pedigree
A = makeA(renumped)
julia> A
12×12 Matrix{Float64}:
1.0 0.0 0.5 0.75 0.5 0.625 0.75 0.6875 0.6875 0.75 0.5 0.84375
0.0 1.0 0.5 0.25 0.5 0.375 0.25 0.3125 0.3125 0.25 0.0 0.15625
0.5 0.5 1.0 0.75 0.5 0.625 0.75 0.6875 0.6875 0.5 0.25 0.59375
0.75 0.25 0.75 1.25 0.5 0.875 0.75 0.8125 0.8125 0.625 0.375 0.78125
0.5 0.5 0.5 0.5 1.0 0.75 0.5 0.625 0.625 0.75 0.25 0.5625
0.625 0.375 0.625 0.875 0.75 1.25 0.625 0.9375 0.9375 0.6875 0.3125 0.78125
0.75 0.25 0.75 0.75 0.5 0.625 1.25 0.9375 0.9375 0.625 0.375 0.84375
0.6875 0.3125 0.6875 0.8125 0.625 0.9375 0.9375 1.3125 0.9375 0.65625 0.34375 1.0
0.6875 0.3125 0.6875 0.8125 0.625 0.9375 0.9375 0.9375 1.3125 0.65625 0.34375 0.8125
0.75 0.25 0.5 0.625 0.75 0.6875 0.625 0.65625 0.65625 1.25 0.375 0.703125
0.5 0.0 0.25 0.375 0.25 0.3125 0.375 0.34375 0.34375 0.375 1.0 0.421875
0.84375 0.15625 0.59375 0.78125 0.5625 0.78125 0.84375 1.0 0.8125 0.703125 0.421875 1.34375
Read your own pedigree
You can download this pedigree here to test this package. Please then change working_dir and data_file to your local directory.
# load CSV
using CSV
# directory and data file name
working_dir = "/Users/austinputz/Documents/ISU/Classes/AnS_562/2023/Julia/"
data_file = "pedigree_MSU.csv"
# load swine data
ped_MSU = CSV.read(working_dir * data_file, # this will just combine the 2 strings
DataFrame,
header=true,
delim=',',
missingstring="NA")
# we can now use this real pedigree to sort, renumber, and calculate A
# sort pedigreee
ped_MSU_sort = sort_ped(ped_MSU)
# renumber pedigree
ped_MSU_renum = renum_ped(ped_MSU_sort)
# calculate A matrix
A = makeA(ped_MSU_renum)
FAQ (frequently asked questions)
You may have a problem downloading Pedigree.jl with XSim.jl, I have alerted Hao Cheng of this situation, but XSim seems to be very behind in it's development to include compatability with new packages. So there is an incompatibility with XSim and key packages like DataFrames. I suggest you remove XSim from your environment until XSim gets updated.
I do suggest trying to learn XSim, but for now you can also try working with that package in it's own environment. Please search how to separate environments and keep a project for only that package with it's old dependencies.