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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