Description Usage Arguments Details Value
gemma2 : GEMMA programme in R (better version of gemma)
1 2 3 4 |
geno |
: genotype –> one row per SNP, and one column per sample. |
pheno |
: phenotype d'interet (doit etre une matrice) |
map |
: This file contains one line per SNP, with |
covar |
: covariable et NULL marche |
gemma.exe |
: the executable gemma |
opt.mat |
: option for the calcul of the related.matrix, "1" calculates the centered relatedness # matrix while "2" calculates the standardized relatedness matrix |
met.reg |
: linear mixed model of Bayesian sparse linear mixed model. |
lmm |
: if lmm choose option : where the "1" performs Wald test "2" performs likelihood ratio test, "3" performs score test, "4" performs all the three tests. |
bslmm |
: if bslmm choose option : "1" fits a standard linear BSLMM "2" fits a ridge regression/GBLUP, "3" fits a probit BSLMM. |
pmin |
: for bslmm : initial no zero proportion of beta (pi) |
pmax |
: for bslmm : max no zero proportion of beta (pi) |
opt.bs |
: option for bslmm : w and s default as in Zeng 2017 (10000 for both) |
smax |
: Number of variants with sparse effects (~ number of major effect loci). Default to 300 like in gemma |
three |
columns: (1) SNP label, (2) base-pair position, (3) chromosome. |
See paper of GEMMA
: a gemma result
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