sim.ibd.var: Create an ibd.var object via simulations using gene-dropping

In ibdreg: Regression Methods for IBD Linkage with Covariates

Create an ibd.var object via simulations using gene-dropping

Description

Create an ibd.var object, containing a mean vector and covariance matrix for the ibd sharing values between each pair of relative pairs in each pedigree. Use a gene-dropping approach with 2 unique alleles for each founder, and simulate n.sim times. Then calculate the moments based on the vector of allele sharing between all relative pairs within the pedigree.

Usage

sim.ibd.var(pedfile, 
            male.code=1, 
            female.code=2, 
            x.linked=FALSE, 
            n.sim=1000, 
            print.resources=FALSE)

Arguments

pedfile	file containing ids for pedigree, person, father, and mother, and gender. Also known as a pre-MAKEPED format file.
male.code	The code that denotes a sex classification of "male".
female.code	The code that denotes a sex classification of "female".
x.linked	A flag that denotes whether the inheritance mode should be autosomal (x.linked=FALSE, the default) or X-linked (x.linked=TRUE).
n.sim	Number of simulations
print.resources	logical, set to TRUE to print CPU and memory usage for calculations on each pedigree.

Details

The bulk of the work for simulating ibd sharing vectors is in sim.mark.prop(). These methods will handle practically any correctly formed pedigree structure. This includes pedigrees containing loops, multiple pairs of ancestoral founders, and both loops and multiple pairs of ancestoral founders. Thus, maximum flexibility may be obtained. Both autosomal and X-linked methods of inheritance are supported through the use of the x.linked parameter.

Value

The return value, call it ret, is an ibd.var object that contains the following elements for each pedigree:

ped.id	pedigree id
person1.id	vector of ids for first person in the relative pair
person2.id	vector of ids for second person in the relative pair
sm	mean vector of ibd sharing between relative pairs: person1.id, person2.id
sv	variance-covariance matrix for ibd sharing between pairs of relative pairs

References

Schaid DJ, Sinnwell JP, Thibodeau SN. Testing Genetic Linkage with Relative Pairs and Covariates by Quasi-Likelihood Score Statistics. Submitted.

See Also

exact.ibd.var, sim.ibd.setup, sim.mark.prop

Examples

## See manual(s) for full example usage
## Below is a basic example for one pedigree
## Not Run:
# Since input parameter is a "pre" file, create a "pre" file for one pedigree

# make a data.frame to write to a file
ped.id <- rep(7,7)
person <- c(1,2,3,4,5,6,7)
father <- c(0,0,0,1,0,3,5)
mother <- c(0,0,0,2,0,4,4)
sex    <- c(1,2,1,2,1,1,1)
chrom1 <- c(1,3,5,0,7,0,0)
chrom2 <- c(2,4,6,0,8,0,0)
ped7.df <- data.frame(ped.id, person, father, mother, 
                     sex, chrom1, chrom2)

# write the file
## Not run: write.table(ped7.df, file="ped7.pre", row.names=FALSE, col.names=FALSE)

## Not run: ped7.ibdVar <- sim.ibd.var("ped7.pre", n.sim=1000)

# results are long and difficult to interpret
# here is an example of how to view
## Not run: print(ped7.ibdVar[[1]], digits=2)

# demonstrate for x.linked=TRUE
## Not run: ped7.ibdVarX <- sim.ibd.var("ped7.pre", n.sim=1000, x.linked=TRUE)

ibdreg documentation built on Nov. 16, 2022, 5:14 p.m.