IsoformSwitchAnalyzeR: object 'analysisAllIsoformsWithoutORF' not found

Question

[VenGeno]

Hi,

I am getting the following error when I try to use analysisAllIsoformsWithoutORF . So I went with the original example provided with the package to check and still got the same error.

object 'analysisAllIsoformsWithoutORF' not found .

The code I used is as follows;

    > extractSwitchSummary(exampleSwitchListAnalyzed)
                   Comparison nrIsoforms nrSwitches nrGenes
        1 hESC vs Fibroblasts         82         58      38
    > analyzeNovelIsoformORF(exampleSwitchListAnalyzed, 
    +                        analysisAllIsoformsWithoutORF, # also analyse all those annoatated as without CDS in ref annottaion
    +                        genomeObject = NULL,
    +                        
    +                        ### Advanced argument
    +                        minORFlength = 100,
    +                        orfMethod = 'longest.AnnotatedWhenPossible',
    +                        PTCDistance = 50,
    +                        startCodons = "ATG",
    +                        stopCodons = c("TAA", "TAG", "TGA"),
    +                        showProgress = TRUE,
    +                        quiet = FALSE
    +                        )
Error in analyzeNovelIsoformORF(exampleSwitchListAnalyzed, analysisAllIsoformsWithoutORF,  : 
  object 'analysisAllIsoformsWithoutORF' not found

I am using version 1.16.0. Can someone help me? Thanks in advance.

Answer 1

[Trivas]

From the website documentation it looks like it's looking for a TRUE/FALSE statement. My guess is you want to use analysisAllIsoformsWithoutORF = TRUE.

[VenGeno]

Thank you Trivas ! 🙏 I mixed up when reading the error . "analyzeNovelIsoformORF" vs "analysisAllIsoformsWithoutORF" . Have a great rest of the day!