Deleted:error with importing Pfam output, isoformswitchanalyzer
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mekili • 0
Last seen 3 months ago

Hi, i am trying to perform some analysis with isoformswitchanalyzer package. i used it before and it worked properly but now when i am trying to import Pfam result file, i get the following error. How can i fix it?

exampleSwitchList <- isoformSwitchAnalysisPart2(
  switchAnalyzeRlist        = exampleSwitchList, 
  dIFcutoff                = 0.5,   # Cutoff for defining switch size - set high for short runtime in example data
  n                         = 300,    # here put as many as differential genes are previously identified
  removeNoncodinORFs        = TRUE,  # Because ORF was predicted de novo
  pathToCPC2resultFile      = "cpc2_LH.txt",
  pathToPFAMresultFile      = "Pfam_LH.txt",
  pathToSignalPresultFile   = "SignalP_LH.txt", 
  pathToIUPred2AresultFile = "IUpred2A_LH.result" ,
  outputPlots               = T,  # keeps the function from outputting the plots from this example
  consequencesToAnalyze = c( 'intron_retention')

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unique': 'seq id  alignment start alignment end   envelope start  envelope end    hmm acc hmm name        hmm start       hmm end hmm length      bit score       Individual E-value      Conditional E-value     database significant    outcompeted     clan' does not exist in current working directory
IsoformSwitchAnalyzeR PFAM.db • 70 views
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