[BioC] Introns in exons and vice versa (Genomic Features)

[Fenton Christopher Graham]

library(GenomicFeatures) 
 
#get known genes 
genes <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene")
saveFeatures(genes, file="hg19_knownGene.sqlite")
txdb    <- loadFeatures("hg19_knownGene.sqlite")

#get introns
introns <- intronsByTranscript(txdb) 
introns <- unlist(introns)

#get exons
exons    <- exonsBy(txdb)
exons    <- unlist(exons)  

#take chr1 and "+" stand 
introns_ind  <- which(seqnames(introns) == "chr1" & strand(introns) == "+") 
exons_ind   <- which(seqnames(exons) == "chr1" & stand(exons) == "+") 

#convert to ranges 
introns_chr1 <- ranges(introns[introns_ind,]) 
exons_chr1   <- ranges(exons[exons_ind,]) 

#look for introns in exons? 
sum(countOverlaps(introns_chr1, exons_chr1, type="within"))

Why isn't this number 0? 
Why are we looking at over 1000 introns within exons? 


Chris