Importing Data from Salmon via Tximeta + isoformSwitchAnalysisPart1 get error 'pathToGTF' argument

[lu lu]

Hey Kristoffer,

I imported my Data from Salmon via Tximeta, then used isoformSwitchAnalysisPart1, but got an error. Here is my script:

salmonDf <- prepareSalmonFileDataFrame("salmonoutput")
salmonDf$condition <- c('FXS','FXS','Control','Control','FXS','FXS','FXS','FXS','Control','Control','Control','Control','Control')
aSwitchList <- importSalmonData(
    salmonFileDataFrame = salmonDf,
    showProgress=FALSE)
aslist <- isoformSwitchAnalysisPart1(switchAnalyzeRlist=aSwitchList,
  pathToOutput = '/isoformsalmontximeta',
    outputSequences      = TRUE,
    prepareForWebServers = TRUE)

The error: Error in isoformSwitchAnalysisPart1(switchAnalyzeRlist = aSwitchList, :

When ORFs are not annotated you must supply the GTF with known annotation to the 'pathToGTF' argument.

Could you please help me?

Best,

Lu