Console Wfccm

Command line aspect of Wfccm. Limited capability extended.

Todo

  • Add support for Shuo's preprocessed data - log transformation not applicable
  • QUESTION? Add support for DataGrouping.MultiLoad?
    • Simplify the DataGrouping file needed
    • Must include the InformationSet
  • Compile and test using Mono on GNULinux

Use

  • wfccm2 -train <-generate> -d dataSet <-l logdataset> -g groupingfile -f filterfile <-r runname>
    • <scores.txt>, means.txt, train_output.txt
  • wfccm2 -test -d dataSet -f filterfile -s scorefile -m meansfile <-g grouping> <-r runname> *test_output.txt

Command Line options

  • -train : Indicates that a training type analysis in going to be done
  • -test : Indicates that a testing type analysis in going to be done
  • <-generate> : Indicates that the program needs to generate scores
  • -d dataSet : path to the data set
  • <-l logdataset> : Path to the log dataset
  • -g groupingfile : path to the grouping file
  • -f filterfile : path to the filter criteria file
  • -s scorefile : path to the score file
  • -m meansfile : path to the distance output means.
  • <-r runname> : optional run name that will be added to the output names.
  • scores.txt : score output file.
  • means.txt : Means output file.
  • train_output.txt : Training output
  • test_output.txt : Testing output

Extended Functionality needed

  1. DataGrouping.Write
  2. DataGrouping.Read
  3. CriteriaSet.Write
  4. CriteriaSet.Read

Defaults

  • Scores to be generated:
    • Sam (sam, asam)
    • Wga (wga)
    • Info (info)
    • TTest (tvalue, prob_t)
    • Fisher (fvalue, prob_f)
    • Wilcox (cvalue, prob_c)
  • Function: (1 - info)*(numPass / 6)*(asam_std + tvalue_std + fvalue_std + cvalue_std)
  • Sign: tvalue will set fvalue, cvalue and asam

This topic: Main > Projects > MicroArrayMassSpec > GeneralWfccmDesign > WfccmCommandLineMethod
Topic revision: 22 Apr 2005, WillGray
 
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