SKED Systems Biology Documentation

SKED Scripts

scpMultiDataTutorial

This script provides examples of the main functions used to explore data stored in the SKED relational database schema. scpMultiDataTutorialE04 includes these functions using E04 as the example dataset.

scpMultiDataLoad

This script loads all the experimental data. scpMultiDataLoadE04 provides the same functions with E04 as the example dataset.  

SKED Functions

funCropImage.m

   In:
     •   filename – output filename
     •   append – option if you would like to resave the image
  Out:
     •   a correctly cropped image
   Example:
    funCropImage(filename,append)

funFormatTimeTick.m

   In:
     •   t = date vector in string format
     •   n = gap in date ticks
  Out:
     •   a formatted time axis
   Example:
    out = funFormatTimeTick(t,n)

funGetExperimentNames.m

   In:
     •   cStructures - MATLAB structure that contains all the data
  Out:
     •   a list of the experiment names
   Example:
    cExperiments = funGetExperimentNames(cStructures);

funGetProtocolData.m

   In:
     •   cStructures - MATLAB structure that contains all the data
     •   sExp – Expermient name; ex. 'E04R'
     •   sSubjects - the name of a subject as a string, ex sSubjects = 'RMe14'; or sSubjects = 'All';
     •   sDataType - the name of the protocol, ex. sDataType = 'Metabolomics';
  Out:
     •   a list of protocol data
   Example:
    funGetProtocol(cStructures,sExp,sSubjects,sDataType)

funGetProtocol.m

   In:
     •   cStructures - MATLAB structure that contains all the data
     •   sExp – Expermient name; ex. 'E04R'
     •   sSubjects - the name of a subject as a string, ex sSubjects = 'RMe14'; or sSubjects = 'All';
     •   sDataType - the name of the protocol, ex. sDataType = 'Metabolomics'
  Out:
     •   a list of available protocols
   Example:
    funGetProtocol(cStructures,sExp,sSubjects,sDataType)

funGetVariableNames.m

   In:
     •   cStructures - MATLAB structure that contains all the data
     •   sExp – Expermient name; ex. 'E04R'
     •   sSubjects - the name of a subject as a string, ex sSubjects = 'RMe14'; or sSubjects = 'All';
     •   sDataType - the name of the protocol, ex. sDataType = 'Metabolomics'
  Out:
     •   a list of variables associated with the specified protocols
   Example:
    funGetVariableNames(cStructures,sExp,sSubjects,sProtocol)

funHodrickPrescott.m

   In:
     •   y - numeric vector, vector to be filtered
     •   lambda - integer, the filtering parameter
  Out:
     •   a smoothed time series as a vector
   Example:
    [s] = funHodrickPrescott(y,lambda)

funLibSizeNormalizationLowCountRemoval.m

   In:
     •   strucData - data structure with parasite genes removed
     •   nCount - the lowest count a gene should have to be considered present
  Out:
     •   a structure with low count genes removed
   Example:
    strucLibSizeNormalizedData = funLibSizeNormalizationLowCountRemoval(strucData,nCount);

funMANOVAPlot.m

   In:
     •   strucData - the data structure containing all the information for the experiments
     •   strucData.Experiment - the experiment names being considered
  Out:
     •   multiple ANOVA analysis
   Example:
    funMANOVAPlot(strucData,strucData.Experiment);

funParasiteGeneRemoval.m

   In:
     •   strucData - a MATLAB data structure containing the functional genomics data, ex. strucData = funGetProtocolData(cStructures,sExp,sSubjects,sProtocol) ;
     •   sIdentifier - gene label associtaed with parasite genes, ex. sIdentifier = 'x_PCOAH';
  Out:
     •   the input functinoal genomics data structure without parasite genes
   Example:
    strucData = funParasiteGeneRemoval(strucData,sIdentifier);

funPlotVariable.m

   In:
     •   cStructures - MATLAB structure that contains all the data
     •   sExp – Expermient name; ex. 'E04R'
     •   sSubjects - the name of a subject as a string, ex sSubjects = 'RMe14'; or sSubjects = 'All';
     •   cVariables - a list of variables to be plotted, ex. cVariables = {'ME_CBC','hgb'};
  Out:
     •   a graph with the desired variables
   Example:
    h = funPlotVariable(cStructures,sExp,sSubjects,cVariables);

funPrintImage.m

   In:
     •   h - a list of the attributes of the ouput graph
     •   sName - the ouput filename
  Out:
     •   a high resolution .jpg file of the graph
   Example:
    sFileName = funPrintImage(h,sName)

funPrintPDF.m

   In:
     •   h - a list of the attributes of the ouput graph
     •   sFileName - the ouput filename
  Out:
     •   a high resolution .pdf file of the graph
   Example:
    funPrintPDF(h,sFileName)

getExperiments.m

   In:
     •   None; make sure that you have added your information to funCredentials.m
  Out:
     •   a list of available experiments
   Example:
     out = getExperiments()