View source: R/functions_for_RGWAS.R
score.calc | R Documentation |
Calculate -log10(p) of each SNP by the Wald test.
score.calc(
M.now,
ZETA.now,
y,
X.now,
package.MM = "gaston",
Hinv,
P3D = TRUE,
eigen.G = NULL,
optimizer = "nlminb",
n.core = 1,
min.MAF = 0.02,
count = TRUE
)
M.now |
A |
ZETA.now |
A list of variance (relationship) matrix (K; |
y |
A |
X.now |
A |
package.MM |
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 |
Hinv |
The inverse of |
P3D |
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. |
eigen.G |
A list with
The result of the eigen decompsition of |
optimizer |
The function used in the optimization process. We offer "optim", "optimx", and "nlminb" functions. This argument is only valid when ‘package.MM = ’RAINBOWR''. |
n.core |
Setting n.core > 1 will enable parallel execution on a machine with multiple cores. |
min.MAF |
Specifies the minimum minor allele frequency (MAF). If a marker has a MAF less than min.MAF, it is assigned a zero score. |
count |
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.
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