Pedigree_Examples

Jason Sinnwell

24 March, 2024

Introduction

This document is a brief tutorial for the kinship2 package, with examples of creating pedigree objects and kinship matrices, and other pedigree utilities. If the kinship2 package is not loaded, we load it now.

require(kinship2)
## Loading required package: kinship2
## Loading required package: Matrix
## Loading required package: quadprog
## Warning: package 'quadprog' was built under R version 4.3.3

Basic Usage

Example Data

Two datasets are provided within the kinship2 package: + minnbreast: 17 families from a breast cancer study + sample.ped: two sample pedigrees, with 41 and 14 subjects

This vignette uses the two pedigrees in sample.ped. For more information on these datasets, see help(minnbreast) and help(sample.ped).

Pedigree

First, we load sample.ped and look at some of the values in the dataset, and create a pedigreeList object using the pedigree() function. We use the required arguments \(id\), \(father\), \(mother\), and \(sex\). The \(famid\) argument is required to make a {} object, but not for a single pedigree} object.

data(sample.ped)
sample.ped[1:10,]
##    ped  id father mother sex affected avail
## 1    1 101      0      0   1        0     0
## 2    1 102      0      0   2        1     0
## 3    1 103    135    136   1        1     0
## 4    1 104      0      0   2        0     0
## 5    1 105      0      0   1       NA     0
## 6    1 106      0      0   2       NA     0
## 7    1 107      0      0   1        1     0
## 8    1 108      0      0   2        0     0
## 9    1 109    101    102   2        0     1
## 10   1 110    103    104   1        1     1
pedAll <- pedigree(id=sample.ped$id, 
                dadid=sample.ped$father, momid=sample.ped$mother, 
                sex=sample.ped$sex, famid=sample.ped$ped)
print(pedAll)
## Pedigree list with 55 total subjects in 2 families

The {} object can be subset to individual pedigrees by their family id. The pedigree object has a print and plot method, which we show below. The print method prints a short summary of the pedigree, while the plot in Figure~\(\ref{basicPed2}\) displays the smaller pedigree.

ped1basic <- pedAll['1']
ped2basic <- pedAll['2']
print(ped1basic)
## Pedigree object with 41 subjects, family id= 1 
## Bit size= 46
print(ped2basic)
## Pedigree object with 14 subjects, family id= 2 
## Bit size= 16
plot(ped2basic)

# plot(ped1basic)

Fixing Pedigree Issues

To “break” the pedigree, we can manipulate the sex value to not match the parent value (in this example, we change \(203\) from a male to a female, even though \(203\) is a father). To do this, we first subset datped2, locate the id column, and match it to a specific id (in this case, \(203\)). Within id \(203\), then locate in the sex column. Assign this subset to the incorrect value of 2 (female) to change the original/correct value of 1 (male).

To further break the pedigree, we can delete subjects who seem irrelevant to the pedigree (in this example, we delete \(209\) because he is a married-in father). To do this, we subset datped2 and use the -which() function to locate and delete the specified subject (in this case, \(209\)). Reassign this code to datped22 to drop the specified subject entirely.

datped2 <- sample.ped[sample.ped$ped %in% 2,]
datped2[datped2$id %in% 203, "sex"] <- 2
datped2 <- datped2[-which(datped2$id %in% 209),]

An error occurs when the pedigree() function notices that id \(203\) is not coded to be male (1) but is a father. To correct this, we simply employ the fixParents() function to adjust the sex value to match either mother/momid or father/dadid. fixParents() will also add back in any deleted subjects, further fixing the pedigree.

tryout <- try({
   ped2 <- with(datped2, pedigree(id, father, mother, sex))
})
## Error in pedigree(id, father, mother, sex) : 
##   Id not male, but is a father: 203
fixped2 <- with(datped2, fixParents(id, father, mother, sex))
fixped2
##     id momid dadid sex
## 1  201     0     0   1
## 2  202     0     0   2
## 3  203     0     0   1
## 4  204   202   201   2
## 5  205   202   201   1
## 6  206   202   201   2
## 7  207   202   201   2
## 8  208   202   201   2
## 9  210   204   203   1
## 10 211   204   203   1
## 11 212   208   209   2
## 12 213   208   209   1
## 13 214   208   209   1
## 14 209     0     0   1
ped2 <- with(fixped2, pedigree(id, dadid, momid, sex))
plot(ped2)

If the fix is straightforward (changing one sex value based on either being a mother or father), fixParents() will resolve the issue. If the issue is more complicated, say if \(203\) is coded to be both a father and a mother, fixParents() will not know which one is correct and therefore the issue will not be resolved.

Kinship

A common use for pedigrees is to make a matrix of kinship coefficients that can be used in mixed effect models. A kinship coefficient is the probability that a randomly selected allele from two people at a given locus will be identical by descent (IBD), assuming all founder alleles are independent. For example, we each have two alleles per autosomal marker, so sampling two alleles with replacement from our own DNA has only \(p=0.50\) probability of getting the same allele twice.

We use {} to calculate the kinship matrix for \(ped2basic\). The result is a special symmetrix matrix class from the Matrix R package, which is stored efficiently to avoid repeating elements.

kin2 <- kinship(ped2basic)
kin2
##       201   202  203   204   205   206   207   208  209    210    211    212    213    214
## 201 0.500 0.000 0.00 0.250 0.250 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
## 202 0.000 0.500 0.00 0.250 0.250 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
## 203 0.000 0.000 0.50 0.000 0.000 0.000 0.000 0.000 0.00 0.2500 0.2500 0.0000 0.0000 0.0000
## 204 0.250 0.250 0.00 0.500 0.250 0.250 0.250 0.250 0.00 0.2500 0.2500 0.1250 0.1250 0.1250
## 205 0.250 0.250 0.00 0.250 0.500 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
## 206 0.250 0.250 0.00 0.250 0.250 0.500 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
## 207 0.250 0.250 0.00 0.250 0.250 0.250 0.500 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
## 208 0.250 0.250 0.00 0.250 0.250 0.250 0.250 0.500 0.00 0.1250 0.1250 0.2500 0.2500 0.2500
## 209 0.000 0.000 0.00 0.000 0.000 0.000 0.000 0.000 0.50 0.0000 0.0000 0.2500 0.2500 0.2500
## 210 0.125 0.125 0.25 0.250 0.125 0.125 0.125 0.125 0.00 0.5000 0.2500 0.0625 0.0625 0.0625
## 211 0.125 0.125 0.25 0.250 0.125 0.125 0.125 0.125 0.00 0.2500 0.5000 0.0625 0.0625 0.0625
## 212 0.125 0.125 0.00 0.125 0.125 0.125 0.125 0.250 0.25 0.0625 0.0625 0.5000 0.2500 0.2500
## 213 0.125 0.125 0.00 0.125 0.125 0.125 0.125 0.250 0.25 0.0625 0.0625 0.2500 0.5000 0.2500
## 214 0.125 0.125 0.00 0.125 0.125 0.125 0.125 0.250 0.25 0.0625 0.0625 0.2500 0.2500 0.5000

For family 2, see that the row and column names match the id in the figure below, and see that each kinship coefficient with themselves is \(0.50\), siblings are \(0.25\) (e.g. \(204-205\)), and pedigree marry-ins only share alleles IBD with their children with coefficient \(0.25\) (e.g. \(203-210\)). The plot can be used to verify other kinship coefficients.

Kinship for pedigreeList object

The kinship function also works on a {} object. We show how to create the kinship matrix, then show a snapshot of them for the two families, where the row and columns names are the ids of the subject.

pedAll <- pedigree(id=sample.ped$id, 
                dadid=sample.ped$father, momid=sample.ped$mother, 
                sex=sample.ped$sex, famid=sample.ped$ped)
kinAll <- kinship(pedAll)
kinAll[1:14,1:14]
## 14 x 14 sparse Matrix of class "dsCMatrix"
##   [[ suppressing 14 column names '101', '102', '103' ... ]]
##                                                                     
## 101 0.50 .    .    .    .   .   .   .   0.25 .    .    .    .   .   
## 102 .    0.50 .    .    .   .   .   .   0.25 .    .    .    .   .   
## 103 .    .    0.50 .    .   .   .   .   .    0.25 0.25 0.25 .   0.25
## 104 .    .    .    0.50 .   .   .   .   .    0.25 0.25 0.25 .   0.25
## 105 .    .    .    .    0.5 .   .   .   .    .    .    .    .   .   
## 106 .    .    .    .    .   0.5 .   .   .    .    .    .    .   .   
## 107 .    .    .    .    .   .   0.5 .   .    .    .    .    .   .   
## 108 .    .    .    .    .   .   .   0.5 .    .    .    .    .   .   
## 109 0.25 0.25 .    .    .   .   .   .   0.50 .    .    .    .   .   
## 110 .    .    0.25 0.25 .   .   .   .   .    0.50 0.25 0.25 .   0.25
## 111 .    .    0.25 0.25 .   .   .   .   .    0.25 0.50 0.25 .   0.25
## 112 .    .    0.25 0.25 .   .   .   .   .    0.25 0.25 0.50 .   0.25
## 113 .    .    .    .    .   .   .   .   .    .    .    .    0.5 .   
## 114 .    .    0.25 0.25 .   .   .   .   .    0.25 0.25 0.25 .   0.50
kinAll[40:43, 40:43]
## 4 x 4 sparse Matrix of class "dsCMatrix"
##      140  141 201 202
## 140 0.50 0.25 .   .  
## 141 0.25 0.50 .   .  
## 201 .    .    0.5 .  
## 202 .    .    .   0.5
kinAll[42:46, 42:46]
## 5 x 5 sparse Matrix of class "dsCMatrix"
##      201  202 203  204  205
## 201 0.50 .    .   0.25 0.25
## 202 .    0.50 .   0.25 0.25
## 203 .    .    0.5 .    .   
## 204 0.25 0.25 .   0.50 0.25
## 205 0.25 0.25 .   0.25 0.50

Kinship for twins in pedigreeList object

Specifying twin relationships in a pedigreeList object is complicated by the fact that the user must specify the family id to which the id1 and id2 belong. We show below the relation matrix requires the family id to be in the last column, with the column names as done below, to make the plotting and kinship matrices to show up with the monozygotic twins correctly. We show how to specify monozygosity for subjects 206 and 207 in sample pedigree 2, and subjects 125 and 126 in pedigree 1. We check it by looking at the kinship matrix for these pairs, which are correctly at \(0.5\).

reltwins <- rbind(c(206, 207, 1, 2), c(125, 126, 1, 1))
colnames(reltwins)=c("id1","id2","code","famid")
pedAll <- with(sample.ped, pedigree(id=id, dadid=father, momid=mother,
  sex=sex, famid=ped, relation=reltwins))
kinAll <- kinship(pedAll)
kinAll[21:31,21:31]
## 11 x 11 sparse Matrix of class "dsCMatrix"
##   [[ suppressing 11 column names '121', '122', '123' ... ]]
##                                                                                 
## 121 0.5000 0.2500 0.2500 0.2500 0.0625 0.0625 0.0625 0.0625 .      .      .     
## 122 0.2500 0.5000 0.2500 0.2500 0.0625 0.0625 0.0625 0.0625 .      .      .     
## 123 0.2500 0.2500 0.5000 0.2500 0.0625 0.0625 0.0625 0.0625 .      .      .     
## 124 0.2500 0.2500 0.2500 0.5000 0.0625 0.0625 0.0625 0.0625 .      .      .     
## 125 0.0625 0.0625 0.0625 0.0625 0.5000 0.5000 0.1250 0.1250 0.0625 0.0625 0.0625
## 126 0.0625 0.0625 0.0625 0.0625 0.5000 0.5000 0.1250 0.1250 0.0625 0.0625 0.0625
## 127 0.0625 0.0625 0.0625 0.0625 0.1250 0.1250 0.5000 0.2500 0.0625 0.0625 0.0625
## 128 0.0625 0.0625 0.0625 0.0625 0.1250 0.1250 0.2500 0.5000 0.0625 0.0625 0.0625
## 129 .      .      .      .      0.0625 0.0625 0.0625 0.0625 0.5000 0.0625 0.0625
## 130 .      .      .      .      0.0625 0.0625 0.0625 0.0625 0.0625 0.5000 0.2500
## 131 .      .      .      .      0.0625 0.0625 0.0625 0.0625 0.0625 0.2500 0.5000
kinAll[42:50,42:50]
## 9 x 9 sparse Matrix of class "dsCMatrix"
##      201  202 203  204  205  206  207  208 209
## 201 0.50 .    .   0.25 0.25 0.25 0.25 0.25 .  
## 202 .    0.50 .   0.25 0.25 0.25 0.25 0.25 .  
## 203 .    .    0.5 .    .    .    .    .    .  
## 204 0.25 0.25 .   0.50 0.25 0.25 0.25 0.25 .  
## 205 0.25 0.25 .   0.25 0.50 0.25 0.25 0.25 .  
## 206 0.25 0.25 .   0.25 0.25 0.50 0.50 0.25 .  
## 207 0.25 0.25 .   0.25 0.25 0.50 0.50 0.25 .  
## 208 0.25 0.25 .   0.25 0.25 0.25 0.25 0.50 .  
## 209 .    .    .   .    .    .    .    .    0.5

Note that subject \(113\) is not in pedigree 1 because they are a marry-in without children in the pedigree. Subject \(113\) is in their own pedigree of size 1 in the \(kinAll\) matrix at index \(41\). We later show how to handle such marry-ins for plotting.

Optional Pedigree Features

We use pedigree 2 from \(sample.ped\) to sequentially add optional information to the pedigree object.

The example below shows how to specify a \(status\) indicator, such as vital status. The \(sample.ped\) data does not include such an
indicator, so we create one to indicate that the first generation of pedigree 2, subjects 1 and 2, are deceased.

df2 <- sample.ped[sample.ped$ped==2,]
names(df2)
## [1] "ped"      "id"       "father"   "mother"   "sex"      "affected" "avail"
df2$censor <- c(1,1, rep(0, 12))
ped2 <- pedigree(df2$id, df2$father, df2$mother, 
                 df2$sex, status=df2$censor)

Affected Indicators

We show how to specify affected status with a single indicator and multiple indicators in a matrix. First, we use the affected indicator from \(sample.ped\), which contains 0/1 indicators and NA as missing, and let it it indicate blue eyes. Next, we create a matrix to contain the affected indicator from \(sample.ped\) and a second indicator that we create, imagine as an indicator for baldness.

ped2 <- pedigree(df2$id, df2$father, df2$mother, 
                 df2$sex, affected=df2$affected,
                 status=df2$censor)
aff2 <- data.frame(blue=df2$affected, 
                   bald=c(0,0,0,0,1,0,0,0,0,1,1,0,0,1))
ped2 <- pedigree(df2$id, df2$father, df2$mother, 
                 df2$sex, affected=as.matrix(aff2),
                 status=df2$censor)

Special Relationships

Special pedigree relationships can be specified in a matrix as the \(relation\) argument. There are 4 relationships that can be specified by numeric codes: 1=Monozygotic twins, 2=Dizygotic twins, 3=Twins of unknown zygosity, and 4=Spouse. The spouse relationship can indicate a marry-in when a couple does not have children together.

Below, we create a matrix of relationships for monozygotic and unknown-zygosity twins in the most recent generation of pedigree 2.

## create twin relationships
relate2 <- matrix(c(210,211,1,
                   212,213,3), nrow=2, byrow=TRUE)
ped2 <- pedigree(df2$id, df2$father, df2$mother, 
                 df2$sex, affected=as.matrix(aff2),
                 status=df2$censor,
                 relation=relate2)

Another special relationship is inbreeding. Inbreeding of founders implies the founders’ parents are related (the maternal and paternal genes descended from a single ancestral gene). One thing we can do is add more people to the pedigree to show this inbreeding.

To show that a pair of founders (subjects \(201\) and \(202\)) are inbred, we must show that their parents are siblings. To do this, we create subjects \(197\) and \(198\) to be the parents of \(201\) and also create subjects \(199\) and \(200\) to be the parents of \(202\). To make subjects \(198\) and \(199\) siblings, we give them the same parents, creating subjects \(195\) and \(196\). This results in subjects \(201\) and \(202\) being first cousins, and therefore inbred.

id <- 195:202
dadid <- c(0,0,0,196,196,0,197,199)
momid <- c(0,0,0,195,195,0,198,200)
sex <- c(2,1,1,2,1,2,1,2)
ped3 <- pedigree(id, dadid, momid, sex)
ped4df <- rbind.data.frame(as.data.frame(ped2)[-c(1,2),1:4], as.data.frame(ped3))
ped4 <- with(ped4df, pedigree(id, dadid, momid, sex))
plot(ped4, cex=.5)

Pedigree Plot Details

The plot method does an admirable job plotting pedigrees within the standard R plotting paradigm. It attempts to adhere to many standards in pedigree plotting, as presented by Bennet et al. 2008.

We show in the following figure, the plot of the updated pedigree 2. The plot shapes for each subject are divided into two equal parts and shaded differently to indicate the two affected indicators. Also, the two deceased subjects are displayed with a diagonal line through the shape. The twin relationships are both represented with diverging lines from a single point. The monozygotic twins have an additional line connecting the diverging lines, while the other twins have a question mark to indicate unknown zygosity.

We also show how the subjects can be colored individually, where we color a subject red if their avail indicator is 1, which can represent their DNA availability, a useful indicator in genetic studies. Lastly, we show how to use the \(id\) argument in the plot method to add additional information under each subject. In the example below, we add names to the existing \(id\) vector using the newline character as the \(sep\) argument in paste(). As space permits, more lines and characters per line can be made using the \(id\) argument.

Finally, we show how a pedigree.legend can place a simple legend in one of the corners of the pedigree plot to show the sections of the plot symbols corresponding to the multiple affected indicators.

id2 <- paste(df2$id, c("John", "Linda", "Jack", "Rachel", "Joe", "Deb", 
                         "Lucy", "Ken", "Barb", "Mike", "Matt", 
                         "Mindy", "Mark", "George"), sep="\n")
plot(ped2, col=ifelse(df2$avail, 2, 1), id=id2, cex=.5)
pedigree.legend(ped2, location="topright", radius=.2)

To show some other tricks with pedigree plotting, we use pedigree 1 from sample.ped, which has 41 subjects in 4 generations, including a generation with double first cousins. After the first marriage of 114, they remarried subject 113 without children between them. If we do not specify the marriage with the \(relation\) argument, the plot method excludes subject \(113\) from the plot. The basic plot of pedigree 1 is shown in the figure below, where the subjects are colored red if their avail indicator is 1.

df1<- sample.ped[sample.ped$ped==1,]
relate1 <- matrix(c(113, 114, 4), nrow=1)
ped1 <- pedigree(df1$id, df1$father, df1$mother, 
       df1$sex, affected=df1$affected, 
                 relation=relate1)
print(ped1)
## Pedigree object with 41 subjects
## Bit size= 46
plot(ped1, col=ifelse(df1$avail==1, "red","black"),cex=.7)

Align by Input Order

The plot method does a decent job aligning subjects given the order of the subjects when the pedigree object is made, and sometimes has to make two copies of a subject. If we change the order of the subjects when creating the pedigree, we can help the plot method reduce the need to duplicate subjects, as Figure~\(\ref{reordPed1}\) no longer has subject \(110\) duplicated.

df1reord <- df1[c(35:41,1:34),]
ped1reord <- pedigree(df1reord$id, df1reord$father, df1reord$mother, 
       df1reord$sex, affected=df1reord$affected, relation=relate1)
plot(ped1reord, col=df1reord$avail+1, cex=.7)

Legend Plot

The legendPlot() function creates a dynamic legend based on the arguments passed through it. First, we give it color names and new labels for the affected status, which is two for blue eyes and baldness that we created previously for ped2.

legendPlot(ped2, col=ifelse(df2$avail, "red", "black"),
   id=id2, symbolsize=.4,
   affected.label=c("blue eyes", "baldness"),
   col.label=c(`black`="no dna", `red`="dna"))

We can do the same plot by giving integer color codes, and a non-named vector of colors. Also, we can let the function grab the colnames() of the affected matrix for the legend.

colnames(ped2$affected)
## [1] "blue" "bald"
legendPlot(ped2, col=ifelse(df2$avail, 2, 1),
   id=id2, cex=.5, symbolsize=.5,
   col.label=c("no dna", "dna"))

Pedigree Utility Functions

Pedigree as a Data.Frame

A main features of a pedigree object are vectors with an element for each subject. It is sometimes useful to extract these vectors from the pedigree object into a \(data.frame\) with basic information that can be used to construct a new pedigree object. This is possible with the \(as.data.frame()\) method, as shown below.

dfped2 <- as.data.frame(ped2)
dfped2
##     id dadid momid    sex affected.blue affected.bald status
## 1  201     0     0   male             1             0      1
## 2  202     0     0 female            NA             0      1
## 3  203     0     0   male             1             0      0
## 4  204   201   202 female             0             0      0
## 5  205   201   202   male            NA             1      0
## 6  206   201   202 female             1             0      0
## 7  207   201   202 female             1             0      0
## 8  208   201   202 female             0             0      0
## 9  209     0     0   male             0             0      0
## 10 210   203   204   male             0             1      0
## 11 211   203   204   male             0             1      0
## 12 212   209   208 female             0             0      0
## 13 213   209   208   male             0             0      0
## 14 214   209   208   male             1             1      0

Subsetting and Trimming

Pedigrees with large size can be a bottleneck for programs that run calculations on them. The kinship2 package contains some routines to identify which subjects to remove. We show how a subject (e.g. subject 210) can be removed from ped2, and how the pedigree object is changed by verifying that the relation matrix no longer has the twin relationship between subjects 210 and 211, as indicated by \(indx1\) and indx2. Also note that the \(relation\) matrix indices are updated for persons 212 and 213 who have index 11 and 12 after subject 210 is removed.

ped2.rm210 <- ped2[-10]
data.frame(ped2.rm210)
##     id dadid momid    sex affected.blue affected.bald
## 1  201     0     0   male             1             0
## 2  202     0     0 female            NA             0
## 3  203     0     0   male             1             0
## 4  204   201   202 female             0             0
## 5  205   201   202   male            NA             1
## 6  206   201   202 female             1             0
## 7  207   201   202 female             1             0
## 8  208   201   202 female             0             0
## 9  209     0     0   male             0             0
## 10 211   203   204   male             0             1
## 11 212   209   208 female             0             0
## 12 213   209   208   male             0             0
## 13 214   209   208   male             1             1
ped2.rm210$relation
##   indx1 indx2    code
## 2    11    12 UZ twin
ped2$relation
##   indx1 indx2    code
## 1    10    11 MZ twin
## 2    12    13 UZ twin

The steps above only work for subsetting by the index of the pedigree object vectors, not by the id of the subjects themselves.
We provide pedigree.trim(), which trims subjects from a pedigree by their \(id\). Below is an example of removing subject 110, as done above, then we further trim the pedigree by a vector of subject ids. We check the trimming by looking at the \(id\) vector and the \(relation\) matrix.

ped2.trim210 <- pedigree.trim(210, ped2)
ped2.trim210$id
##  [1] 201 202 203 204 205 206 207 208 209 211 212 213 214
ped2.trim210$relation
##   indx1 indx2    code
## 2    11    12 UZ twin
ped2.trim.more <- pedigree.trim(c(212,214), ped2.trim210)
ped2.trim.more$id
##  [1] 201 202 203 204 205 206 207 208 209 211 213
ped2.trim.more$relation
## NULL

Shrinking

An additional function in kinship2 is pedigree.shrink(), which shrinks a pedigree to a specified bit size while maintaining the maximal amount of information for genetic linkage and association studies. Using an indicator for availability and affected status, it removes subjects in this order: + unavailable with no available descendants + available and are not parents + available who have missing affected status + available who are unaffected + available who are affected

We show how to shrink pedigree 1 to bit size \(30\), which happens to be the bit size after removing only the unavailable subjects. We show how to extract the shrunken pedigree object from the \(pedigree.shrink\) result, and plot it.

set.seed(200)
shrink1.B30 <- pedigree.shrink(ped=ped1,
                 avail=df1$avail, maxBits=30)
print(shrink1.B30)
#plot.pedigree.shrink(shrink1.B30, col=shrink1.B30$avail + 1, cex=.6)

Now shrink pedigree 1 to bit size \(25\), which requires removing subjects who are informative. If there is a tie between multiple subjects about who to remove, the method randomly chooses one of them. With this seed setting, the method removes subjects \(126\) then \(125\).

set.seed(10)
shrink1.B25 <- pedigree.shrink(ped=ped1, avail=df1$avail, 
                               maxBits=25)
shrink1.B25
#plot.pedigree.shrink(shrink1.B25, col=shrink1.B25$avail+1, cex=.6)

Select Unrelateds

In this section we briefly show how to use \(pedigree.unrelated\) to find a set of the maximum number of unrelated available subjects from a pedigree. The input required is a pedigree object and a vector indicating availability. In some pedigrees there are numerous sets of subjects that satisfy the maximum number of unrelateds, so the method randomly chooses from the set. We show two sets of subject ids that are selected by the routine and discuss below.

df2<- sample.ped[sample.ped$ped==2,]
ped2 <- pedigree(df2$id, df2$father, df2$mother, 
       df2$sex, affected=df2$affected)
set.seed(10)
set1 <- pedigree.unrelated(ped2, avail=df2$avail)
set1
## [1] "203" "206"
set2 <- pedigree.unrelated(ped2, avail=df2$avail)
set2
## [1] "203" "214"

We can easily verify the sets selected by \(pedigree.unrelated\) by referring to Figure~\(\ref{basicPed2}\) and see that subjects 203 and 209 are unrelated to everyone else in the pedigree except their children. Furthermore, we see in df2 that of these two, only subject 203 is available. Therefore, any set of unrelateds who are available must include subject 203 and one of the these subjects: 201, 204, 206, 207, 212, and 214, as indicated by the kinship matrix for pedigree 2 subset to those with availability status of 1.

df2
##    ped  id father mother sex affected avail
## 42   2 201      0      0   1        1     1
## 43   2 202      0      0   2       NA     0
## 44   2 203      0      0   1        1     1
## 45   2 204    201    202   2        0     1
## 46   2 205    201    202   1       NA     0
## 47   2 206    201    202   2        1     1
## 48   2 207    201    202   2        1     1
## 49   2 208    201    202   2        0     0
## 50   2 209      0      0   1        0     0
## 51   2 210    203    204   1        0     0
## 52   2 211    203    204   1        0     1
## 53   2 212    209    208   2        0     1
## 54   2 213    209    208   1        0     0
## 55   2 214    209    208   1        1     1
kin2[df2$avail==1,df2$avail==1]
##       201  203   204   206   207    211    212    214
## 201 0.500 0.00 0.250 0.250 0.250 0.1250 0.1250 0.1250
## 203 0.000 0.50 0.000 0.000 0.000 0.2500 0.0000 0.0000
## 204 0.250 0.00 0.500 0.250 0.250 0.2500 0.1250 0.1250
## 206 0.250 0.00 0.250 0.500 0.250 0.1250 0.1250 0.1250
## 207 0.250 0.00 0.250 0.250 0.500 0.1250 0.1250 0.1250
## 211 0.125 0.25 0.250 0.125 0.125 0.5000 0.0625 0.0625
## 212 0.125 0.00 0.125 0.125 0.125 0.0625 0.5000 0.2500
## 214 0.125 0.00 0.125 0.125 0.125 0.0625 0.2500 0.5000