kinship_last_gen {simfam} | R Documentation |
Calculate kinship matrix for last generation of a pedigree with structured founders
Description
A wrapper around the more general kinship_fam()
, specialized to save memory when only the last generation is desired (kinship_fam()
returns kinship 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
kinship_last_gen(kinship, fam, ids, missing_vals = c("", 0))
Arguments
kinship |
The kinship matrix of the founders.
This matrix must have column and row names that identify each founder (matching codes in |
fam |
The pedigree data.frame, in plink FAM format.
Only columns |
ids |
A list containing vectors of IDs for each generation.
All these IDs must be present in |
missing_vals |
The list of ID values treated as missing.
|
Value
The kinship matrix of the last generation (the intersection of ids[ length(ids) ]
and fam$id
).
The columns/rows of this matrix are last-generation individuals in the order that they appear in fam$id
.
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') )
# 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 kinship matrix of the children
kinship2 <- kinship_last_gen( kinship, fam, ids )
kinship2