cic: Calculate Jacquard condensed identity coefficients

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

Calculate Jacquard condensed identity coefficients

Description

Calculate Jacquard condensed identity coefficients from a pedigree.

Usage

cic(ped, ids, inter, df=3, ask = FALSE, msg = FALSE)

Arguments

ped	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	IDs of the individuals for which to calculate the Jacquard condensed identity coefficients. If missing, all individuals in the pedigree ped will be considered.
inter	Intermediate generations, if given, where coefficients are calculated bottom-up.
df	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.
ask	If true, users will be asked whether to proceed.
msg	If true, will print out some messages.

Details

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.

Value

A matrix G with G[,j] being the j-th Jacquard identity coefficients.

Note

You may need the administrative privilege to run this function on systems such as Windows 7. It may require your operating system support "long long" integer type in C++. If you run this function in a windows system, make sure the working directory is under system volume C and you have the write privilege.

It is better to remove the working directory if the program is interrupted by external forces (e.g. killed by users).

Warning: you may need to run this program on a 64-bit machine in case of seeing such a message!

References

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.

See Also

pedRecode for more information.

Examples

data(miscEx)

ids<- sample(pedF8$id[300:500],20)

## Not run: 
# 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))

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.