This is one method that might work.
#Melt matrix and then convert to data.table object
yourmatrix <- melt(yourmatrix)[melt(upper.tri(yourmatrix))$value,]
names(yourmatrix) <- c("v1", "v2", "value")
yourmatrix <- data.table(yourmatrix)
#Setkeys and reference quickly
setkey(yourmatrix,v1,v2)
yourmatrix[J("B","C")]
--
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