List of 25
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-i"
.. ..@ long_flag : chr "--inputFile"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "inputFile"
.. ..@ default : chr ""
.. ..@ help : chr "I/O: Input file: Progenesis (Feature,Protein or Peptide) .csv,\n\t\t\tor Scaffold Q+ (Raw Export, for TMT quant) .xls (REQUIRE"| __truncated__
.. ..@ metavar : chr "inputFile"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-o"
.. ..@ long_flag : chr "--outputDir"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "outputDir"
.. ..@ default : chr NA
.. ..@ help : chr "I/O: Results Output Directory [default FOLDER OF INPUTFILE]"
.. ..@ metavar : chr "outputDir"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-l"
.. ..@ long_flag : chr "--resultsFileLabel"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "resultsFileLabel"
.. ..@ default : chr "SQ_Results"
.. ..@ help : chr "I/O: results file directory [default %default]"
.. ..@ metavar : chr "resultsFileLabel"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-f"
.. ..@ long_flag : chr "--fastaFile"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "fastaFile"
.. ..@ default : chr ""
.. ..@ help : chr "I/O: Protein DB .fasta file [default ./]"
.. ..@ metavar : chr "fastaFile"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-p"
.. ..@ long_flag : chr "--scaffoldPTMSpectrumReportFile"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "scaffoldPTMSpectrumReportFile"
.. ..@ default : chr ""
.. ..@ help : chr "I/O: Scaffold PTM Spectrum Report File [default ./]"
.. ..@ metavar : chr "scaffoldPTMSpectrumReportFile"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FProteinAccessionSelection"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "FProteinAccessionSelection"
.. ..@ default : chr "."
.. ..@ help : chr "FILTER: --FP Filter features by Accession Regular Expression [default %default] (all features kept)"
.. ..@ metavar : chr "Protein Accession Reg. expr."
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FModificationSelection"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "FModificationSelection"
.. ..@ default : chr ""
.. ..@ help : chr "FILTER (LFQ PEP ONLY): --FM Only keep Peptides with modifications matching Regular Expression [default %default]\n\t\t\t\t (all"| __truncated__
.. ..@ metavar : chr "modification name Reg. expr."
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FFdrCutoff"
.. ..@ action : chr "store"
.. ..@ type : chr "double"
.. ..@ dest : chr "FFdrCutoff"
.. ..@ default : num 0.01
.. ..@ help : chr "FILTER (LFQ ONLY): --FF Identification level False Discovery Rate Cutoff. [0-1] [default %default]"
.. ..@ metavar : chr "Peptide/Protein FDR cutoff"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FCoefficientOfVarianceMax"
.. ..@ action : chr "store"
.. ..@ type : chr "double"
.. ..@ dest : chr "FCoefficientOfVarianceMax"
.. ..@ default : num Inf
.. ..@ help : chr "FILTER: --FC Do not include features with C.V. above this threshold in statistical \n\t\t\t\ttest for differential expression ["| __truncated__
.. ..@ metavar : chr "Coefficent of Variance cutoff"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FDeltaMassTolerancePrecursor"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "FDeltaMassTolerancePrecursor"
.. ..@ default : chr "AUTO SET"
.. ..@ help : chr "FILTER (LFQ PEP ONLY): --FD Precursor mass Error Range filter (ppm) [default %default].\n\t\t\t\tPeptide imports ONLY"
.. ..@ metavar : chr "Mass Range [x,y]"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FNumberOfPeptidesPerProteinMin"
.. ..@ action : chr "store"
.. ..@ type : chr "integer"
.. ..@ dest : chr "FNumberOfPeptidesPerProteinMin"
.. ..@ default : int 1
.. ..@ help : chr "FILTER: --FN Only include those proteins with at least x identified peptides [default %default]\n\t\t\t\tProtein analysis ONLY."| __truncated__
.. ..@ metavar : chr "Number of peptides"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FSitesPerPeptide"
.. ..@ action : chr "store"
.. ..@ type : chr "integer"
.. ..@ dest : chr "FSitesPerPeptide"
.. ..@ default : int 99999
.. ..@ help : chr "FILTER: --FS Max Nb. Modifications Per Peptide [default Inf]\n\t\t\t\t\t\tPeptide analysis ONLY."
.. ..@ metavar : chr "Max Number of PTM sites Per Petptide"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--FLengthPeptide"
.. ..@ action : chr "store"
.. ..@ type : chr "integer"
.. ..@ dest : chr "FLengthPeptide"
.. ..@ default : int 1
.. ..@ help : chr "FILTER: --FL Min Peptide Length (Nb. AA's) [default Inf]\n\t\t\t\t\t\tPeptide analysis ONLY."
.. ..@ metavar : chr "Min Peptide Length (>=)"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--SAnchorProtein"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "SAnchorProtein"
.. ..@ default : chr "."
.. ..@ help : chr "STATISTICS: --SA Normalize Intensities by selected protein(s) Regular Expression\n\t\t\t [default %default] (use all proteins)."| __truncated__
.. ..@ metavar : chr "Protein Accession Reg. expr."
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--SPvalueInclude"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "SPvalueInclude"
.. ..@ default : logi FALSE
.. ..@ help : chr "STATISTICS: --SP output eBayes moderated t-statistic p-values [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--SNonPairWiseStatTest"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "SNonPairWiseStatTest"
.. ..@ default : logi FALSE
.. ..@ help : chr "STATISTICS: --SN non pairwise eBayes moderated t-statistic p-values [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--EXperimentalDesign"
.. ..@ action : chr "store"
.. ..@ type : chr "character"
.. ..@ dest : chr "EXperimentalDesign"
.. ..@ default : chr NA
.. ..@ help : chr "EXPERIMENTAL DESIGN: --EX \",\" seperated samples, \":\" separated conditions \n\t\t\t\t\tExample: 1,2,3:4,5,6 \n\t\t\t\t\t c"| __truncated__
.. ..@ metavar : chr "EXperimentalDesign"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--EProteinQuantOff"
.. ..@ action : chr "store_false"
.. ..@ type : chr "logical"
.. ..@ dest : chr "EProteinQuantOff"
.. ..@ default : logi TRUE
.. ..@ help : chr "EXPERIMENTAL DESIGN: --EP Disable Protein Level Quantification [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--PRatioCutOff"
.. ..@ action : chr "store"
.. ..@ type : chr "double"
.. ..@ dest : chr "PRatioCutOff"
.. ..@ default : num 1
.. ..@ help : chr "PDF-REPORT: --PR Intensity ratio (fold change) cut-off used for graphics export. >1 [default %default]"
.. ..@ metavar : chr "Intensity ratio cutoff"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--PQvaueCutOff"
.. ..@ action : chr "store"
.. ..@ type : chr "double"
.. ..@ dest : chr "PQvaueCutOff"
.. ..@ default : num 0.01
.. ..@ help : chr "PDF-REPORT: --PQ Qvalue cut-off used for graphics. \n\t\t\tHigh-lighting features with a qval < specified value. [0-1] [default"| __truncated__
.. ..@ metavar : chr "Differential expression qvalue cutOff"
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--ARDataFile"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "ARDataFile"
.. ..@ default : logi FALSE
.. ..@ help : chr "ADDITIONAL-REPORTS: --AR Save R objects in 'label'.RData file [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--AIbaq"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "AIbaq"
.. ..@ default : logi FALSE
.. ..@ help : chr "ADDITIONAL-REPORTS (LFQ PROT): --AI creates .tsv output file\n\t\t\t\t\tincluding protein iBAQ values. [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr NA
.. ..@ long_flag : chr "--ATop3"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "ATop3"
.. ..@ default : logi FALSE
.. ..@ help : chr "ADDITIONAL-REPORTS (LFQ PEP): --AT creates .tsv output file\n\t\t\t\t\tincluding protein top3 values. [default %default]"
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-t"
.. ..@ long_flag : chr "--test"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "test"
.. ..@ default : logi FALSE
.. ..@ help : chr "TEST: test option, include first 2000 entries only [default %default]\n\t\t\tPeptide analysis ONLY."
.. ..@ metavar : chr(0)
$ :Formal class 'OptionParserOption' [package "optparse"] with 8 slots
.. ..@ short_flag: chr "-v"
.. ..@ long_flag : chr "--verbose"
.. ..@ action : chr "store_true"
.. ..@ type : chr "logical"
.. ..@ dest : chr "verbose"
.. ..@ default : logi FALSE
.. ..@ help : chr "Print extra output [default %default]"
.. ..@ metavar : chr(0)