Simulating Pedigree
-Unlike Tolstoy, where only happy families are alike, all pedigrees -are alike. Moreover, such pedigrees can be simulated as a function of -several parameters, including the number of children per mate, -generations, sex ratio of newborns, and mating rate
-The simulation function provides users the opportunity to test family -models in pedigrees with a customized pedigree length and width. Since -data in the form of large family pedigrees is difficult to collect or -access, simulated pedigrees serve as an efficient tool for building -statistical models using family data and evaluating the statistical -properties of the model, such as power, bias, and computational +
Simulating Pedigrees
+Unlike Tolstoy, where only happy families are alike, all
+pedigrees are alike – or at least, all simulated pedigrees are alike.
+The simulatePedigree function generates a pedigree with a
+user-specified number of generations and individuals per generation.
+This function provides users the opportunity to test family models in
+pedigrees with a customized pedigree length and width.
These pedigrees can be simulated as a function of several parameters, +including the number of children per mate, generations, sex ratio of +newborns, and mating rate. Given that large family pedigrees are +difficult to collect or access, simulated pedigrees serve as an +efficient tool for researchers. These simulated pedigrees are useful for +building family-based statistical models, and evaluating their +statistical properties, such as power, bias, and computational efficiency.
-For example, a pedigree that follows these conditions: There are a -total of four generations in which each mating produces four offspring. -The number of male and female newborns is equal. 70% of individuals mate -and bear offspring. Such a pedigree structure can be simulated by +
To illustrate this, let us generate a pedigree. This pedigree has a +total of four generations, in which each person who “mates”, grows a +family with four offspring. In our scenario, the number of male and +female newborns is equal. In this illustration 70% of individuals will +mate and bear offspring. Such a pedigree structure can be simulated by running:
set.seed(5)
-Ped <- SimPed(kpc = 4, Ngen = 4, sexR = .5, marR = .7)
-
-summary(Ped)
-#> fam ID gen dadID
-#> Length:57 Min. : 10011 Min. :1.000 Min. : 10012
-#> Class :character 1st Qu.: 10036 1st Qu.:3.000 1st Qu.: 10024
-#> Mode :character Median :100312 Median :3.000 Median : 10037
-#> Mean : 59171 Mean :3.298 Mean : 42859
-#> 3rd Qu.:100416 3rd Qu.:4.000 3rd Qu.:100311
-#> Max. :100432 Max. :4.000 Max. :100320
-#> NA's :13
-#> momID spt sex
-#> Min. : 10011 Min. : 10011 Length:57
-#> 1st Qu.: 10022 1st Qu.: 10025 Class :character
-#> Median : 10036 Median : 10036 Mode :character
-#> Mean : 42859 Mean : 40124
-#> 3rd Qu.:100316 3rd Qu.:100311
-#> Max. :100318 Max. :100320
-#> NA's :13 NA's :33The simulation output is a data.frame with 57 rows and 7
columns. Each row corresponds to a simulated individual.
Ped[21, ]
+
The columns represents the individual’s family ID, the individual’s
@@ -410,10 +416,10 @@
Single Pedigree Visualization
To visualize a single simulated pedigree, use the
plotPedigree() function.
# Plot the simulated pedigree
-plotPedigree(Ped)
+plotPedigree(df_ped)
#> Pedigree object with 57 subjects, family id= 1
#> Bit size= 75
-
+
#> Did not plot the following people: 10032
In the resulting plot, biological males are represented by squares,
while biological females are represented by circles, following the
@@ -425,10 +431,10 @@
Visualizing Multiple Pedigrees Side-by-Side
them together. For instance, let’s visualize pedigrees for families
spanning three and four generations, respectively.
# Simulate a family with 3 generations
-df_ped_3 <- SimPed(Ngen = 3)
+df_ped_3 <- simulatePedigree(Ngen = 3)
# Simulate a family with 4 generations
-df_ped_4 <- SimPed(Ngen = 4)
+df_ped_4 <- simulatePedigree(Ngen = 4)
# Set up plotting parameters for side-by-side display
par(mfrow = c(1, 2))
@@ -442,7 +448,7 @@ Visualizing Multiple Pedigrees Side-by-Side
plotPedigree(df_ped_4, width = 1)
#> Pedigree object with 29 subjects, family id= 1
#> Bit size= 34
-
+
By examining the side-by-side plots, you can contrast and analyze the
structures of different families, tracing the inheritance of specific
traits or conditions if needed.