Hi,

I am looking to get the intron length per transcript using the package GenomicFeatures and a gff file.

This is what I got so far:

library(GenomicFeatures)
library(rtracklayer)

txdb <- makeTxDbFromGFF(file = "data.gff", format = "gff")
introns <- intronsByTranscript(txdb)

# mean, median all intron
i <- unlist(introns)
summary(width(i))

So I am able to get the length of all introns but not the length of combined intron per transcript.

Any help please ?

Thanks

sum(width(introns))

Have a look at: looping through a GRangesList object In short, though:

uli = unlist(introns)
iwidths = width(uli)
lintrons = relist(iwidths, introns)
head(lintrons)

The sum of intron lengths per transcript:

intron_length_per_transcript = sapply(lintrons, sum)