RVT2(y, X, maf = 0.05, perm = 100)
maf=0.05
by default)"assoctest"
, basically a list with the following elements:
maf
threshold, the function will stop and return an error message There is no imputation for the missing data. Missing values are simply ignored in the computations.
Asimit J, Zeggini E (2010) Rare Variant Association Analysis Methods for Complex Traits. Annual Review of Genetics, 44: 293-308
RVT1
## Not run:
#
# # number of cases
# cases = 500
#
# # number of controls
# controls = 500
#
# # total (cases + controls)
# total = cases + controls
#
# # phenotype vector
# phenotype = c(rep(1, cases), rep(0, controls))
#
# # genotype matrix with 10 variants (random data)
# set.seed(1234)
# genotype = matrix(rbinom(total*10, 2, 0.051), nrow=total, ncol=10)
#
# # apply RVT2 with maf=0.05 and 500 permutations
# myrvt2 = RVT2(phenotype, genotype, maf=0.05)
# myrvt2
# ## End(Not run)
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