score.calc: Calculate -log10(p) for single-SNP GWAS

View source: R/functions_for_RGWAS.R

score.calcR Documentation

Calculate -log10(p) for single-SNP GWAS


Calculate -log10(p) of each SNP by the Wald test.


  package.MM = "gaston",
  P3D = TRUE,
  eigen.G = NULL,
  optimizer = "nlminb",
  n.core = 1,
  min.MAF = 0.02,
  count = TRUE


A n \times m genotype matrix where n is sample size and m is the number of markers.

A list of variance (relationship) matrix (K; m \times m) and its design matrix (Z; n \times m) of random effects. You can use only one kernel matrix. For example, ZETA = list(A = list(Z = Z, K = K)) Please set names of list "Z" and "K"!


A n \times 1 vector. A vector of phenotypic values should be used. NA is allowed.

A n \times p matrix. You should assign mean vector (rep(1, n)) and covariates. NA is not allowed.


The package name to be used when solving mixed-effects model. We only offer the following three packages: "RAINBOWR", "MM4LMM" and "gaston". Default package is 'gaston'. See more details at EM3.general.


The inverse of H = ZKZ' + \lambda I where \lambda = \sigma^2_e / \sigma^2_u.


When P3D = TRUE, variance components are estimated by REML only once, without any markers in the model. When P3D = FALSE, variance components are estimated by REML for each marker separately.


A list with


Eigen values


Eigen vectors

The result of the eigen decompsition of G = ZKZ'. You can use "spectralG.cpp" function in RAINBOWR. If this argument is NULL, the eigen decomposition will be performed in this function. We recommend you assign the result of the eigen decomposition beforehand for time saving.


The function used in the optimization process. We offer "optim", "optimx", and "nlminb" functions. This argument is only valid when ‘package.MM = ’RAINBOWR''.


Setting n.core > 1 will enable parallel execution on a machine with multiple cores.


Specifies the minimum minor allele frequency (MAF). If a marker has a MAF less than min.MAF, it is assigned a zero score.


When count is TRUE, you can know how far RGWAS has ended with percent display.


-log10(p) for each marker


Kennedy, B.W., Quinton, M. and van Arendonk, J.A. (1992) Estimation of effects of single genes on quantitative traits. J Anim Sci. 70(7): 2000-2012.

Kang, H.M. et al. (2008) Efficient Control of Population Structure in Model Organism Association Mapping. Genetics. 178(3): 1709-1723.

Kang, H.M. et al. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet. 42(4): 348-354.

Zhang, Z. et al. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet. 42(4): 355-360.

RAINBOWR documentation built on July 4, 2024, 1:11 a.m.