1. How to tidy a pedigree

Pedigrees play an important role in animal selective breeding programs. On the one hand, pedigree information can improve the accuracy of estimated breeding values. On the other hand, it helps control inbreeding and avoid inbreeding depression. Therefore, reliable and accurate pedigree records are essential for any selective breeding program. In addition, pedigrees are typically stored in a three-column format (individual, sire, and dam), which makes it difficult to visualize ancestors and descendants. Consequently, visualizing individual pedigrees is highly beneficial. For the Windows platform, Professor Yang Da’s team at the University of Minnesota developed pedigraph, a software for displaying individual pedigrees. It can handle pedigrees containing many individuals. While powerful, it requires configuration via a parameter file. Professor Brian Kinghorn at the University of New England developed pedigree viewer, which can trim, prune, and visually display pedigrees in a windowed interface. However, if the number of individuals is very large, they may overlap. Thus, pedigree visualization functions require further optimization. In the R environment, packages like pedigree, nadiv, and optiSel provide pedigree preparation functions. Packages such as kinship2 and synbreed can also be used to draw pedigree trees. However, these trees often suffer from significant overlapping when the number of individuals is large.

To address this, we developed the visPedigree package. Built on data.table and igraph, it offers robust data cleaning and social network visualization capabilities, significantly enhancing pedigree tidying and visualization. With this package, users can trace and prune ancestors and descendants across multiple generations. It automatically optimizes the pedigree tree layout and can quickly display pedigrees with over 10,000 individuals per generation by compacting full-sib groups and using outlined displays. The main contents of this guide are as follows:

1. Installation of the visPedigree package

The visPedigree package can be installed from CRAN:

install.packages("visPedigree")

Or from GitHub:

# install.packages("devtools")
devtools::install_github("luansheng/visPedigree")

2. Pedigree format specification

The first three columns of pedigree data must be in the order of individual, sire, and dam IDs. The column names can be customized, but their order must remain unchanged. Individual IDs should not be coded as "", " ", "0", *, or NA; otherwise, they will be removed from the pedigree. Missing parents should be denoted by NA, 0, or *. Spaces and empty strings ("") will also be treated as missing parents, though this is not recommended. Additional columns, such as sex and generation, can also be included.

3. Checking and tidying pedigree

3.1 Introduction

The pedigree can be checked and tidied through the tidyped() function.

This function takes a pedigree, checks for duplicates and bisexual individuals, detects loops, adds missing founders, sorts the pedigree, and traces candidate pedigrees.

If the cand parameter is provided, only those individuals and their ancestors or descendants are retained.

Tracing direction and the number of generations can be specified using the trace and tracegen parameters.

Virtual generations are inferred and assigned when addgen = TRUE.

A numeric pedigree is generated when addnum = TRUE.

Sex will be inferred for all individuals if sex information is missing. If a Sex column is present, values should be coded as 'male', 'female', or NA (unknown). Missing sex information will be inferred from the pedigree structure where possible.

The visPedigree package comes with multiple datasets. You can check through the following command.

data(package="visPedigree")

The following code displays the simple_ped dataset, which contains four columns: individual, sire, dam, and sex. Missing parents are denoted by 'NA', '0', or *. Founders are not explicitly listed, and some parents appear after their offspring in the original data.

head(simple_ped)
#>        ID   Sire    Dam    Sex
#>    <char> <char> <char> <char>
#> 1: J4Y326 J3Y620 J3Y771   male
#> 2: J1H419 J0Z938 J0Z167 female
#> 3: J2F588     NA J1Z417 female
#> 4: J1J576 J0Z938 J0Z843   male
#> 5: J1C802 J0Z333 J0C355   male
#> 6: J2Z411 J1X971 J1J134 female
tail(simple_ped)
#>        ID   Sire    Dam    Sex
#>    <char> <char> <char> <char>
#> 1: J1E852 J0Z848 J0Z624 female
#> 2: J1H604 J0C583 J0Z380 female
#> 3: J5X804 J4Y326 J4E185 female
#> 4: J1I438 J0Z990 J0Z808   male
#> 5: J2C808 J1I975 J1F266   male
#> 6: J1K462 J0C317 J0C450 female
# The number of individuals in the pedigree dataset
nrow(simple_ped)
#> [1] 31
# Individual records with missing parents
simple_ped[Sire %in% c("0", "*", "NA", NA) |
             Dam %in% c("0", "*", "NA", NA)]
#>        ID   Sire    Dam    Sex
#>    <char> <char> <char> <char>
#> 1: J2F588     NA J1Z417 female
#> 2: J1J858 J0Z060      * female
#> 3: J3X697 J2Z903      0 female

Example: If we incorrectly set the female J0Z167 as the sire of J2F588, tidyped() will detect this bisexual conflict.

x <- data.table::copy(simple_ped)
x[ID == "J2F588", Sire := "J0Z167"]
y <- tidyped(x)
#> Warning in validate_and_prepare_ped(ped): Bisexual individuals found (both Sire
#> and Dam): J0Z167

The tidyped() function sorts the pedigree, replaces missing parents with NA, ensures parents precede their offspring, and adds missing founders.

tidy_simple_ped <- tidyped(simple_ped)
head(tidy_simple_ped)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int>
#> 1: J0C032   <NA>   <NA> female     1      1       0      0
#> 2: J0C185   <NA>   <NA> female     1      2       0      0
#> 3: J0C231   <NA>   <NA> female     1      3       0      0
#> 4: J0C317   <NA>   <NA>   male     1      4       0      0
#> 5: J0C450   <NA>   <NA> female     1      5       0      0
#> 6: J0C561   <NA>   <NA>   male     1      6       0      0
tail(tidy_simple_ped)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int>
#> 1: J1C802 J0Z333 J0C355   male     5     54      47     46
#> 2: J4E185 J3L886 J3X697 female     5     55      48     49
#> 3: J4Y326 J3Y620 J3Y771   male     5     56      50     51
#> 4: J1C929 J0Z511 J0Z444   male     6     57      53     52
#> 5: J2Y434 J1C802 J1H419 female     6     58      54     28
#> 6: J5X804 J4Y326 J4E185 female     6     59      56     55
nrow(tidy_simple_ped)
#> [1] 59

In the resulting tidy_simple_ped, founders are added with their inferred sex, and parents are sorted before their offspring. The number of individuals increases from 31 to 59. The columns are renamed to Ind, Sire, and Dam. Missing parents are uniformly replaced with NA, and tidyped() provides informative messages during processing. By default, tidy_simple_ped includes new columns: Gen, IndNum, SireNum, and DamNum. These can be disabled by setting addgen = FALSE and addnum = FALSE.

If the input dataset lacks a Sex column, it will be automatically added to the tidied output.

tidy_simple_ped_no_gen_num <-
  tidyped(simple_ped, addgen = FALSE, addnum = FALSE)
    head(tidy_simple_ped_no_gen_num)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex
#>    <char> <char> <char> <char>
#> 1: J0Z938   <NA>   <NA>   male
#> 2: J0Z333   <NA>   <NA>   male
#> 3: J0C561   <NA>   <NA>   male
#> 4: J0Z475   <NA>   <NA>   male
#> 5: J0Z511   <NA>   <NA>   male
#> 6: J0Z664   <NA>   <NA>   male

Once tidied, you can use data.table::fwrite() to export the pedigree for genetic evaluation software like ASReml.

3.2 Pedigree loop detection

A pedigree loop occurs when an individual is its own ancestor (e.g., A is the parent of B, B is the parent of C, and C is the parent of A). This is a biological impossibility and a serious error in pedigree records. The tidyped() function automatically detects these cycles using graph theory algorithms. If a loop is detected, the function will stop and provide information about the individuals involved in the loop.

The following code demonstrates what happens when a pedigree with loops is processed:

# loop_ped contains cycles (e.g., V -> T -> R -> P -> M -> V)
# Attempting to tidy it will result in an error
try(tidyped(loop_ped))
#> Error : Pedigree error! Pedigree loops detected:
#>  M -> P -> R -> T -> V -> M
#> F -> E -> C -> A -> F

Detecting loops early is crucial for ensuring the integrity of genetic evaluations.

When saving the pedigree, missing parents should typically be replaced with 0.

saved_ped <- data.table::copy(tidy_simple_ped)
saved_ped[is.na(Sire), Sire := "0"]
saved_ped[is.na(Dam), Dam := "0"]
data.table::fwrite(
  x = saved_ped,
  file = tempfile(fileext = ".csv"),
  sep = ",",
  quote = FALSE
)

3.3 Tracing the pedigree of a specific individual

To trace the pedigree of specific individuals, use the cand parameter. This adds a Cand column where TRUE identifies the specified candidates. If cand is provided, only the candidates and their ancestors/descendants are retained.

tidy_simple_ped_J5X804_ancestors <-
  tidyped(ped = tidy_simple_ped_no_gen_num, cand = "J5X804")
  tail(tidy_simple_ped_J5X804_ancestors)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum   Cand
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int> <lgcl>
#> 1: J3X697 J2Z903   <NA> female     4     45      43      0  FALSE
#> 2: J3Y620 J2C161 J2Z411   male     4     46      37     42  FALSE
#> 3: J3Y771 J2G465 J2X544 female     4     47      40     41  FALSE
#> 4: J4E185 J3L886 J3X697 female     5     48      44     45  FALSE
#> 5: J4Y326 J3Y620 J3Y771   male     5     49      46     47  FALSE
#> 6: J5X804 J4Y326 J4E185 female     6     50      49     48   TRUE

By default, the function traces ancestors. You can limit the number of generations using tracegen. If tracegen is NULL, all available generations are traced.

tidy_simple_ped_J5X804_ancestors_2 <-
  tidyped(ped = tidy_simple_ped_no_gen_num,
  cand = "J5X804",
  tracegen = 2)
  print(tidy_simple_ped_J5X804_ancestors_2)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum   Cand
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int> <lgcl>
#> 1: J3L886   <NA>   <NA>   male     1      1       0      0  FALSE
#> 2: J3X697   <NA>   <NA> female     1      2       0      0  FALSE
#> 3: J3Y620   <NA>   <NA>   male     1      3       0      0  FALSE
#> 4: J3Y771   <NA>   <NA> female     1      4       0      0  FALSE
#> 5: J4E185 J3L886 J3X697 female     2      5       1      2  FALSE
#> 6: J4Y326 J3Y620 J3Y771   male     2      6       3      4  FALSE
#> 7: J5X804 J4Y326 J4E185 female     3      7       6      5   TRUE

The code above traces the ancestors of J5X804 back two generations.

To trace descendants, set trace = 'down'.

There are three options for the trace parameter:

“up”-trace candidates’ pedigree to ancestors;
“down”-trace candidates’ pedigree to descendants;
“all”-trace candidaes’ pedigree to ancestors and descendants simultaneously.

tidy_simple_ped_J0Z990_offspring <-
  tidyped(ped = tidy_simple_ped_no_gen_num, cand = "J0Z990", trace = "down")
  print(tidy_simple_ped_J0Z990_offspring)
#> Tidy Pedigree Object
#> Index: <Sex>
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum   Cand
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int> <lgcl>
#> 1: J0Z990   <NA>   <NA>   male     1      1       0      0   TRUE
#> 2: J1I438 J0Z990   <NA>   male     2      2       1      0  FALSE
#> 3: J2G465 J1I438   <NA>   male     3      3       2      0  FALSE
#> 4: J3Y771 J2G465   <NA> female     4      4       3      0  FALSE
#> 5: J4Y326   <NA> J3Y771   male     5      5       0      4  FALSE
#> 6: J5X804 J4Y326   <NA> female     6      6       5      0  FALSE

Tracing the descendants of J0Z990 reveals a total of 5 individuals.

3.4 Creating an integer pedigree

Certain genetic evaluation programs require integer-coded pedigrees, where individuals are numbered consecutively to facilitate the calculation of the additive genetic relationship matrix.

By default, tidyped() adds IndNum, SireNum, and DamNum columns. This can be disabled with addnum = FALSE.

tidy_simple_ped_with_int <-
  tidyped(ped = tidy_simple_ped_no_gen_num, addnum = TRUE)
head(tidy_simple_ped_with_int)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int>
#> 1: J0C032   <NA>   <NA> female     1      1       0      0
#> 2: J0C185   <NA>   <NA> female     1      2       0      0
#> 3: J0C231   <NA>   <NA> female     1      3       0      0
#> 4: J0C317   <NA>   <NA>   male     1      4       0      0
#> 5: J0C450   <NA>   <NA> female     1      5       0      0
#> 6: J0C561   <NA>   <NA>   male     1      6       0      0

3.5 Calculating inbreeding coefficients

The inbreeding coefficient (F) of each individual can be calculated using tidyped() or inbreed() functions. There are two options to add the inbreeding coefficients to a tidied pedigree:

Set inbreed = TRUE in the tidyped() function. This will calculate the inbreeding coefficients using the nadiv package and add an f column to the tidied pedigree.
Or call inbreed() directly on a tidied pedigree to add the f column.

# Create a simple inbred pedigree
library(data.table)
test_ped <- data.table(
  Ind = c("A", "B", "C", "D", "E"),
  Sire = c(NA, NA, "A", "C", "C"),
  Dam = c(NA, NA, "B", "B", "D"),
  Sex = c("male", "female", "male", "female", "male")
)
# Option 1: Calculate during tidying
tidy_test <- tidyped(test_ped, inbreed = TRUE)
head(tidy_test)
#> Tidy Pedigree Object
#>       Ind   Sire    Dam    Sex   Gen IndNum SireNum DamNum     f
#>    <char> <char> <char> <char> <int>  <int>   <int>  <int> <num>
#> 1:      A   <NA>   <NA>   male     1      1       0      0 0.000
#> 2:      B   <NA>   <NA> female     1      2       0      0 0.000
#> 3:      C      A      B   male     2      3       1      2 0.000
#> 4:      D      C      B female     3      4       3      2 0.250
#> 5:      E      C      D   male     4      5       3      4 0.375

# Option 2: Calculate after tidying
tidy_test <- inbreed(tidyped(test_ped))

3.6 Summarizing the pedigree

The summary() method provides a quick overview of the pedigree statistics, including the number of individuals, sex distribution, founders, and isolated individuals. If inbreeding coefficients have been calculated (column f), the summary will also include descriptive statistics of inbreeding.

# Summarize the tidied pedigree
summary(tidy_simple_ped)
#> Pedigree Summary:
#> -----------------
#> Total Individuals:  59 
#>   - Males:    29 
#>   - Females:  30 
#> 
#> Founders (parents unknown):  28 
#> Maximum Generation:  6

# Summarize with inbreeding info
summary(tidy_test)
#> Pedigree Summary:
#> -----------------
#> Total Individuals:  5 
#>   - Males:    3 
#>   - Females:  2 
#> 
#> Founders (parents unknown):  2 
#> Maximum Generation:  4 
#> 
#> Inbreeding coefficients:
#>   - All:        Mean=0.1250, Min=0.0000, Max=0.3750