gistfile1.txt

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
t <- transcriptsBy(txdb, by="gene")
e <- exonsBy(txdb, by="tx")
t2 <- unlist(t)
gene2t <- data.frame(gene=names(t2), tx=t2$tx_id)
g <- unique(names(t2))
set.seed(1)
random.genes <- sample(g, 2000, replace=FALSE)
set.seed(1)
length.res <- sapply(random.genes, function(gene) {
  txs <- gene2t$tx[gene2t$gene == gene]
  if (length(txs) == 1) return(1)
  lengths <- sum(width(e[txs]))
  two <- sample(lengths, 2, replace=FALSE)
  two[1]/two[2]
})
set.seed(1)
shared.res <- sapply(random.genes, function(gene) {
  txs <- gene2t$tx[gene2t$gene == gene]
  if (length(txs) == 1) return(1)
  two <- sample(e[txs], 2, replace=FALSE)
  longer <- max(sum(width(two)))
  intersection <- sum(width(intersect(two[[1]], two[[2]])))
  intersection/longer
})
round(quantile(length.res,c(.05,.1,.25,.5,.75,.9,.95)),3)
round(median(shared.res),3)