Deleted:error with importing Pfam output, isoformswitchanalyzer
0
0
Entering edit mode
mekili • 0
@9b7b8554
Last seen 3 months ago
Finland

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
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 832 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6