get mRNAs by TxDb

Question

[hasani.iut6]

Hi everyone.

I'm using transcripts() function in R environment to obtain transcript of Human from TxDb.Hsapiens.UCSC.hg38.knownGene package. I don't know that this transcripts contain intron or not. On the other word, are these transcripts mRNA or not?

tnx all,

Mansoor.

Answer 1

[benformatics]

The transcripts() function will return coordinates for the entire range of a given transcript including introns. To get only the exonic regions use exonsBy()

## known exons for each transcript
exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene,'tx')

## known exons for each gene
exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene,'gene')