R: score statistics for testing genetic linkage of quantitative...

comp.score {gap} | R Documentation

## score statistics for testing genetic linkage of quantitative trait

### Description

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.

### 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.

### Details

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

1. It works with selected nuclear families

2. Trait data on parents (one parent or two parents), if available, are utilized.

3. 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).

### Value

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

### Note

Adapt from score2.r.

### Author(s)

Yingwei Peng, Kai Wang

### References

Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and Nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58:1347-1363

Kruglyak L, Lander ES (1998) Faster multipoint linkage analysis using Fourier transforms J Comp Bio 1998 5:1-7

Wang K (2005) A likelihood approach for quantitative-trait-locus mapping with selected pedigrees. Biometrics 61:465-473

### Examples

    ## Not run:
    # 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(path.package("gap"),"tests/comp.score")
    setwd(cs.dir)
    dir()
    # system("gh < gh.inp")
    cs.default <- comp.score()
    setwd(cwd)

    ## End(Not run)

[Package gap version 1.2.3-6 Index]