score statistics for testing genetic linkage of quantitative trait
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":
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).
comp.score(ibddata="ibd_dist.out", phenotype="pheno.dat", mean=0,
var=1, h2=0.3)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 |
a matrix with each row containing the location and the statistics and their p-values.
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
Adapt from score2.r
Yingwei Peng, Kai Wang
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.