admix_fam {simfam}

Calculate admixture matrix of a pedigree with known admixture of founders

Description

Calculates a full admixture proportions matrix (for all individuals in the provided pedigree FAM table) starting from the admixture proportions of the founders as provided.

Usage

admix_fam(admix, fam, missing_vals = c("", 0))

Arguments

admix

The admixture proportions matrix of the founders (individuals along rows and ancestries along columns). This matrix must have row names that identify each founder (matching codes in fam$id). Individuals may be in a different order than fam$id. Extra individuals in admix but absent in fam$id will be silently ignored. All values should be non-negative and each row of admix should sum to one; for speed, this code does not check that admix is valid, just averages data as-is.

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).

Value

The admixture proportions matrix of the entire fam table, based on the admixture of the founders. These are expectations, calculated for each individual as the average ancestry proportion of the parents. The rows of this admixture matrix correspond to fam$id in that order. The columns (ancestries) are the same as in the input admix.

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')
)

# admixture proportions of the parents
admix <- rbind( c(0.3, 0.3, 0.4), c(0.5, 0.25, 0.25) )
# Name the parents with same codes as in `fam`
# (order can be different)
rownames( admix ) <- c('mother', 'father')
# name ancestries too
colnames( admix ) <- c('African', 'European', 'Asian')

# Calculate the full admixture proportions matrix
admix_all <- admix_fam( admix, fam )

# This is a 3x3 matrix with row names matching fam$id.
# The parent submatrix equals the input (reordered),
# but now there's admixture to the child too (averages of parents)
admix_all