simfam (version 1.1.6)

kinship_fam: Calculate kinship matrix of a pedigree with structured founders

Description

Calculates a full kinship matrix (between all individuals in the provided pedigree FAM table) taking into account the relatedness of the founders as provided. Output agrees with kinship2::kinship() but only when founders are unrelated/outbred (in other words, that function does not allow relatedness between founders).

Usage

kinship_fam(kinship, fam, missing_vals = c("", 0))

Value

The kinship matrix of the entire fam table, taking the relatedness of the founders into account. The rows and columns of this kinship matrix correspond to fam$id in that order.

Arguments

kinship

The kinship matrix of the founders. This matrix must have column and row names that identify each founder (matching codes in fam$id). Individuals may be in a different order than fam$id. Extra individuals in kinship but absent in fam$id will be silently ignored. A traditional pedigree calculation would use kinship = diag(n)/2 (plus appropriate column/row names), where n is the number of founders, to model unrelated and outbred founders. However, if kinship measures the population kinship estimates between founders, the output is also a population kinship matrix (which combines the structural/ancestral and local/pedigree relatedness values into one).

fam

The pedigree data.frame, in plink FAM format. Only columns id, pat, and mat are required. id must be unique and non-missing. Founders must be present, and their pat and mat values must be missing (see below). Non-founders must have both their parents be non-missing. Parents must appear earlier than their children in the table.

missing_vals

The list of ID values treated as missing. NA is always treated as missing. By default, the empty string ('') and zero (0) are also treated as missing (remove values from here if this is a problem).

See Also

Plink FAM format reference: https://www.cog-genomics.org/plink/1.9/formats#fam

Examples

# The smallest pedigree, two parents and a child.
# A minimal fam table with the three required columns.
# Note "mother" and "father" have missing parent IDs, while "child" does not
library(tibble)
fam <- tibble(
  id = c('father', 'mother', 'child'),
  pat = c(NA, NA, 'father'),
  mat = c(NA, NA, 'mother')
)

# Kinship of the parents, here two unrelated/outbred individuals:
kinship <- diag(2)/2
# Name the parents with same codes as in `fam`
# (order can be different)
colnames( kinship ) <- c('mother', 'father')
rownames( kinship ) <- c('mother', 'father')
# For a clearer example, make the father slightly inbred
# (a self-kinship value that exceeds 1/2):
kinship[2,2] <- 0.6

# Calculate the full kinship matrix
kinship_all <- kinship_fam( kinship, fam )

# This is a 3x3 matrix with row/col names matching fam$id.
# The parent submatrix equals the input (reordered),
# but now there's relatedness to the child too
kinship_all