geno_fam {simfam}

Draw random genotypes on a pedigree with known founder genotypes

Description

Constructs a random genotype matrix (for all individuals in the provided pedigree FAM table) starting from the genotype matrix of the founders as provided.

Usage

geno_fam(X, fam, missing_vals = c("", 0))

Arguments

X

The genotype matrix of the founders (loci along rows, individuals along columns). This matrix must have column 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 in c(0L, 1L, 2L); for speed, this code does not check that X is valid (i.e. fractional values between 0 and 2 may not cause errors).

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 random genotype matrix of the entire fam table, starting from the genotypes of the founders. The columns of this matrix correspond to fam$id in that order. The rows (loci) are the same as in the input X.

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')
)

# genotypes of the parents at 4 loci
X <- cbind( c(1, 2, 0, 2), c(0, 2, 2, 1) )
# Name the parents with same codes as in `fam`
# (order can be different)
colnames( X ) <- c('mother', 'father')
# name loci too
rownames( X ) <- paste0( 'rs', 1:4 )

# Draw the full genotype matrix
X_all <- geno_fam( X, fam )

# This is a 4x3 matrix with column names matching fam$id.
# The parent submatrix equals the input (reordered),
# but now there's random genotypes for the child too
X_all