score statistics for testing genetic linkage of quantitative trait

Usage

comp.score(
  ibddata = "ibd_dist.out",
  phenotype = "pheno.dat",
  mean = 0,
  var = 1,
  h2 = 0.3
)

Arguments

ibddata: The output file from GENEHUNTER using command "dump ibd". The default file name is \(ibd_dist.out\).
phenotype: The file of pedigree structure and trait value. The default file name is "pheno.dat". Columns (no headings) are: family ID, person ID, father ID, mother ID, gender, trait value, where Family ID and person ID must be numbers, not characters. Use character "NA" for missing phenotypes.
mean: (population) mean of the trait, with a default value of 0.
var: (population) variance of the trait, with a default value of 1.
h2: heritability of the trait, with a default value of 0.3.

Value

a matrix with each row containing the location and the statistics and their p-values.

Details

The function empirically estimate the variance of the score functions. The variance-covariance matrix consists of two parts: the additive part and the part for the individual-specific environmental effect. Other reasonable decompositions are possible.

This program has the following improvement over "score.r":

It works with selected nuclear families
Trait data on parents (one parent or two parents), if available, are utilized.
Besides a statistic assuming no locus-specific dominance effect, it also computes a statistic that allows for such effect. It computes two statistics instead of one.

Function "merge" is used to merge the IBD data for a pair with the transformed trait data (i.e., \(w_kw_l\)).

Note

Adapt from score2.r.

References

Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996). “Parametric and nonparametric linkage analysis: a unified multipoint approach.” Am J Hum Genet, 58(6), 1347-63.

Kruglyak L, Lander ES (1998). “Faster multipoint linkage analysis using Fourier transforms.” J Comput Biol, 5(1), 1-7. doi:10.1089/cmb.1998.5.1 .

Wang K (2005). “A likelihood approach for quantitative-trait-locus mapping with selected pedigrees.” Biometrics, 61(2), 465-73. doi:10.1111/j.1541-0420.2005.031213.x .

Author

Yingwei Peng, Kai Wang

Examples

if (FALSE) { # \dontrun{
# An example based on GENEHUNTER version 2.1, with quantitative trait data in file
# "pheno.dat" generated from the  standard normal distribution. The following
# exmaple shows that it is possible to automatically call GENEHUNTER using R
# function "system".

cwd <- getwd()
cs.dir <- file.path(find.package("gap"),"tests/comp.score")
setwd(cs.dir)
dir()
# system("gh < gh.inp")
cs.default <- comp.score()
setwd(cwd)
} # }