RBT {AssotesteR} | R Documentation |
The Replication-Based Test has been proposed by Ionita-Laza et al (2011). RBT is based on a weighted-sum statistic that is similar to a pooled association test but purposefully designed to deal with possibly different association directions. The significance of the statistic has to be calculated by permutations.
RBT(y, X, perm = 100)
y |
numeric vector with phenotype status: 0=controls, 1=cases. No missing data allowed |
X |
numeric matrix or data frame with genotype data coded as 0, 1, 2. Missing data is allowed |
perm |
positive integer indicating the number of permutations (100 by default) |
There is no imputation for the missing data. Missing values are simply ignored in the computations.
An object of class "assoctest"
, basically a list with the following elements:
rbt.stat |
rbt statistic |
perm.pval |
permuted p-value |
args |
descriptive information with number of controls, cases, variants, and permutations |
name |
name of the statistic |
Gaston Sanchez
Ionita-Laza I, Buxbaum JD, Laird NM, Lange C (2011) A New Testing Strategy to Identify Rare Variants with Either risk or Protective Effects on Disease. PLoS Genetics, 7(2): e1001289
## 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(123) genotype = matrix(rbinom(total*10, 2, 0.05), nrow=total, ncol=10) # apply RBT with 500 permutations myrbt = RBT(phenotype, genotype, perm=500) myrbt ## End(Not run)