make_kinship_network: Convert pedigree to network

In samellisq/comparekin: Calculating relatedness in biological data

Description

make_kinship_network Creates a kinship network from a pedigree data frame created by the function make_relation_df.

Usage

make_kinship_network(relation.data.frame)

Arguments

relation.data.frame

a data frame produced by the make_relation_df function.

Details

The object returned is the population pedigree represented as a network. This network underlies much of the subsequent relatedness analysis, and is used to both limit the depth of the pedigree and find pairs where relatedness is unknown.

Value

An igraph network object with nodes as all ids in the population (including parents) and directed edges representing parent –> offspring relationships.

Examples

# Example data taken from kinship2::kinship()
test1 <- data.frame(id  =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
                   mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6,  2,  0,  0, 12, 13),
                   dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3,  7,  0,  0, 11, 10),
                   sex =c(0, 1, 0, 1, 0, 1, 0, 1, 0,  0,  0,  1,  1,  1))
#some renaming
names(test1)[2] = "mother"
names(test1)[3] = "father"
test1$sex = ifelse(test1$sex ==1, "F", "M")
test1$id = as.character(test1$id)
test1$mother = ifelse(test1$mother!=0, as.character(test1$mother), "UNK")
test1$father = ifelse(test1$father!=0, as.character(test1$father), "UNK")
test1

r.df = make_relation_df(test1)
net = make_kinship_network(r.df)
plot(net)

samellisq/comparekin documentation built on Dec. 22, 2021, 10:11 p.m.