
Calculate Jacquard condensed identity coefficients from a pedigree.
cic(ped, ids, inter, df=3, ask = FALSE, msg = FALSE)
A matrix G with G[,j] being the j-th Jacquard identity coefficients.
A pedigree, which is a data frame (id, father/sire, mother/dam, ...). If given, "generation" can be numeric 0, 1, 2, ... or non-numeric "F0", "F1", "F2", ... If "sex" is included, male should be "M", "Male" or 1, and female should be "F", "Female" or 2 (other than 0 and 1). If a founder is inbred, its ID should be tagged by character 'i' (e.g. 1i, 2i, etc.). Note: 0 is reserved for unknown father
, mother
or sex
.
IDs of the individuals for which to calculate the Jacquard condensed identity coefficients. If missing, all individuals in the pedigree ped
will be considered.
Intermediate generations, if given, where coefficients are calculated bottom-up.
If inter
is missing, df
is used to derive (optimal) inter
. If df = 0
, then there will no intermediate generations. If df
is large (and free disk space is sufficient), then all generations will be used as intermediate generations.
If true, users will be asked whether to proceed.
If true, will print out some messages.
The coefficients will be calculated for individuals with IDs specified by ids
. All individuals will be considered if ids
is missing. This is not recommended if the total number of individuals in the pedigree is large. Instead, it is recommended that ids
is specified for interested individuals only
df
is a tuning parameter. It should not be 0 (or smaller than 1) if the pedigree is large in depth (many generations) but the number of individuals is not small; otherwise, it can take forever to finish. It should not be Inf
(or a large number) if the number of individuals in certain intermediate generation is very large.
Any individual without parent information is regarded as diallelic with two independent alleles. Users can add to their pedigree (e.g. 50 generations of selfing) if founders are inbred.
Abney, M., M. S. McPeek, and C. Ober (2000). Estimation of variance components of quantitative traits in inbred populations. Am. J. Hum. Genet. 141, 629-650.
pedRecode
for more information.
data(miscEx)
ids<- sample(pedF8$id[300:500],20)
if (FALSE) {
# run 'cic' for the sampled individuals
# top-down
oo<- cic(pedF8, ids=ids, df=Inf, msg=TRUE)
# bottom-up
o1<- cic(pedF8, ids=ids, df=0, msg=TRUE)
# hybrid of top-down and bottom-up
o2<- cic(pedF8, ids=ids, ask=TRUE, msg=TRUE)
# same results
c(sum(abs(oo-o1) >1e-7),sum(abs(o2-o1) >1e-7))
}
Run the code above in your browser using DataLab