Ravages (version 1.1.3)

Jaccard: Jaccard index

Description

Calculates the Jaccard index for each pair of individuals using a bed.matrix

Usage

Jaccard(x, maf.threshold = 0.01)

Value

A squared matrix giving the Jaccard index for each pair of individuals

Arguments

x

A bed.matrix

maf.threshold

The MAF used for the definition of a rare variant, set at 0.01 by default

Details

The individuals carrying no rare variants will have a null Jaccard index with all the individuals including themselves.

References

Jaccard, P. (1908) Nouvelles researches sur la distribution florale, Bulletin de la Société vaudoise des sciences naturelles, 44, 223-270

Examples

# \donttest{
#Simulation of genetic data with GRR values according to the SKAT formula
GRR.del <- GRR.matrix(GRR = "SKAT", genes.maf = Kryukov, 
                      n.case.groups = 2, select.gene = "R1",
                      GRR.multiplicative.factor=2)

#Simulation of one group of 1,000 controls and two groups of 500 cases, 
#50% of causal variants, 5 genomic regions are simulated.
x <- rbm.GRR(genes.maf=Kryukov, size = c(1000, 500, 500),
             prev = c(0.001, 0.001), select.gene = "R1", 
             GRR.matrix.del = GRR.del, p.causal = 0.5,
             genetic.model = "multiplicative", replicates = 5)
                           
#Calculate the Jaccard matrix
J <- Jaccard(x, maf.threshold = 0.01)
# }