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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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UTR length #204

Closed lananh-ngn closed 1 year ago

lananh-ngn commented 1 year ago

Hello, Is there any way to extract UTR length when there is a shortening or a lengthening of the UTRs? Thanks in advance.

kvittingseerup commented 1 year ago

Yep - analyzeSwitchConsequences can do that for you. Check the details in the description of the function 🙂

lananh-ngn commented 1 year ago

Hello, thank you for your fast reply. Sorry if I should have opened a new issue, but I kept looking for it, and I can only see that you can test for whether there are significant changes in UTR length, but not extraction of the UTR length. Thanks in advance.

kvittingseerup commented 1 year ago

Ahh sorry - I was to quick and only say you were interested in them - not you wanted to extract them.

There is not a build-in function for extracting that, so you will have to do some work yourself.

You can find the switches in exampleSwitchListAnalyzed$switchConsequence. You can find the ORF info in exampleSwitchListAnalyzed$orfAnalysis And you can extract the transcript length from the exon entry by summing the width of all exons belonging to an isoform.

Hope this helps 🙂