geno_last_gen {simfam}

Draw random genotypes for last generation of a pedigree with known founder genotypes

Description

A wrapper around the more general geno_fam(), specialized to save memory when only the last generation is desired (geno_fam() returns genotypes for the entire pedigree in a single matrix). This function assumes that generations are non-overlapping (met by the output of sim_pedigree()), in which case each generation g can be drawn from generation g-1 data only. That way, only two consecutive generations need be in memory at any given time. The partitioning of individuals into generations is given by the ids parameter (again matches the output of sim_pedigree()).

Usage

geno_last_gen(X, fam, ids, 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.

ids

A list containing vectors of IDs for each generation. All these IDs must be present in fam$id. If IDs in fam and ids do not fully agree, the code processes the IDs in the intersection, which is helpful when fam is pruned but ids is the original (larger) set.

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 last generation (the intersection of ids[ length(ids) ] and fam$id). The columns of this matrix are last-generation individuals in the order that they appear in fam$id. 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

# A small pedigree, two parents and two children.
# A minimal fam table with the three required columns.
# Note "mother" and "father" have missing parent IDs, while children do not
library(tibble)
fam <- tibble(
  id = c('father', 'mother', 'child', 'sib'),
  pat = c(NA, NA, 'father', 'father'),
  mat = c(NA, NA, 'mother', 'mother')
)
# need an `ids` list separating the generations
ids <- list( c('father', 'mother'), c('child', 'sib') )

# 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 genotype matrix of the children
X2 <- geno_last_gen( X, fam, ids )
X2