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java.lang.Object | +--MJAbase | +--MJAexprProfile
MAExplorer Open Java API class to access expression profiles methods and data structures.
This contains methods for manipulating expression profile data for particular genes across a list of samples. If there are duplicate spots/sample (i.e. F1, F2), then it will also compute the (mean, StdDev, CoeffOvVar) for each sample.
List of methods available to Plugin-writers ----------------- HP-E Expression Profile Modifier Parameters ---------------- getNormToMaxMeanFlag() - normalize expression profile to 1.0 using max Mean getDoMeanPlotsFlag() - generate mean plots (of clusters) else individual plots getEPmaxMeanSampleData() - max mean normalized sample data scale factor getComputedMaxMeanEP() - max mean of the current EP sample data getNormToMaxMeanFlag() - normalize expression profile to 1.0 using max Mean setDoMeanPlotsFlag() - generate mean plots (of clusters) else individual plots setEPmaxMeanSampleData() - max mean normalized sample data scale factor ---------------- Access HP-E Expression Profile Data For Single Gene ------------- calcExprProfile() - compute expression profile of HP-E samples for MID getEPsamplesData() - list of normalized HP-E samples data for MID getEPsamplesMean() - opt. list of normalized HP-E samples means data if dups for MID getEPsamplesStdDev() - opt. list of normalized HP-E samples StdDev if dups for MID getEPsamplesCV() - opt. list of normalized HP-E samples CoeffOfVar if dups for MID ---------------- Access HP-E Expression Profile Data For List of Genes ------------- getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs getListsOfEPsamplesCOF() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs ------ Access Ordered Condition List Expression Profile Data For Single Gene ------ calcOrderedCondListExprProfile() - computes the data for mid and ordered condition list getLastorderedCondListName() - name of last ordered condition list computation getListsOfOrderedCondListMeans() - last means from ordered condition list computation getListsOfOrderedCondListStdDevs() - last StdDevs from ordered condition list computation getListsOfOrderedCondListCVs() - last CVs from ordered condition list computation getListsOfOrderedCondListNbrs() - last cond sizes from ordered condition list computation getListsOfOrderedCondListNames() - last names from ordered condition list computation
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
Method Summary | |
boolean |
calcExprProfile(int mid)
calcExprProfile() - compute expression profile of HP-E samples for MID The data is then returned using other methods. |
boolean |
calcOrderedCondListExprProfile(java.lang.String orderedCondListName,
int mid)
calcOrderedCondListExprProfile() - compute normalized ordered condition list EPs for MID. |
float |
getComputedMaxMeanEP()
getComputedMaxMeanEP() - max mean of the current EP sample data |
boolean |
getDoMeanPlotsFlag()
getDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots |
float |
getEPmaxMeanSampleData()
getEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles. |
float[] |
getEPsamplesCV(int mid)
getEPsamplesCV() - opt. |
float[] |
getEPsamplesData(int mid)
getEPsamplesData() - list of normalized HP-E samples data for MID. |
float[] |
getEPsamplesMean(int mid)
getEPsamplesMean() - opt. |
float[] |
getEPsamplesStdDev(int mid)
getEPsamplesStdDev() - opt. |
java.lang.String |
getLastorderedCondListName()
getLastorderedCondListName() - get name of last ordered condition list computation computed using calcOrderedCondListExprProfile(). |
float[][] |
getListsOfEPsamplesCV(int[] midList)
getListsOfEPsamplesCV() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs. |
float[][] |
getListsOfEPsamplesData(int[] midList)
getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs. |
float[][] |
getListsOfEPsamplesMean(int[] midList)
getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs Compute expression profiles for all of the mid's in the midList[] that are legal (i.e. |
float[][] |
getListsOfEPsamplesStdDev(int[] midList)
getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs. |
float[] |
getListsOfOrderedCondListCVs()
getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from ordered condition list computation computed using calcOrderedCondListExprProfile(). |
float[] |
getListsOfOrderedCondListMeans()
getListsOfOrderedCondListMeans() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile(). |
java.lang.String[] |
getListsOfOrderedCondListNames()
getListsOfOrderedCondListNames() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile(). |
int[] |
getListsOfOrderedCondListNbrs()
getListsOfOrderedCondListNbrs() is last conditions sizes [] from ordered condition list computation computed using calcOrderedCondListExprProfile(). |
float[] |
getListsOfOrderedCondListStdDevs()
getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition list computation computed using calcOrderedCondListExprProfile(). |
boolean |
getNormToOneFlag()
getNormToOneFlag() - flag of normalize expression profile to 1.0 flag |
void |
setDoMeanPlotsFlag(boolean doMeanPlotsFlag)
setDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots |
void |
setEPmaxMeanSampleData(float maxMeanSampleData)
setEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles. |
void |
setNormToOneFlag(boolean normToOneFlag)
setNormToOneFlag() - flag of normalize expression profile to 1.0 flag |
Methods inherited from class MJAbase |
cvtHashtable2SimpleTable, cvtTable2Hashtable |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
public final boolean getNormToOneFlag()
public final boolean getDoMeanPlotsFlag()
public final float getEPmaxMeanSampleData()
public final float getComputedMaxMeanEP()
public final void setNormToOneFlag(boolean normToOneFlag)
public final void setDoMeanPlotsFlag(boolean doMeanPlotsFlag)
doMeanPlotsFlag
- value to set flagpublic final void setEPmaxMeanSampleData(float maxMeanSampleData)
maxMeanSampleData
- value to setpublic final boolean calcExprProfile(int mid)
mid
- is the Master Gene Index to use in compouting expression profilegetEPsamplesData(int)
,
getEPsamplesMean(int)
,
getEPsamplesStdDev(int)
,
getEPsamplesCV(int)
public final float[] getEPsamplesData(int mid)
mid
- (optionl) Master Gene Index to use in compouting expression profilegetEPsamplesMean(int)
,
getEPsamplesStdDev(int)
,
getEPsamplesCV(int)
public final float[] getEPsamplesMean(int mid)
mid
- (optionl) Master Gene Index to use in compouting expression profilegetEPsamplesData(int)
,
getEPsamplesStdDev(int)
,
getEPsamplesCV(int)
public final float[] getEPsamplesStdDev(int mid)
mid
- (optionl) Master Gene Index to use in compouting expression profilegetEPsamplesData(int)
,
getEPsamplesMean(int)
,
getEPsamplesCV(int)
public final float[] getEPsamplesCV(int mid)
mid
- (optionl) Master Gene Index to use in compouting expression profilegetEPsamplesData(int)
,
getEPsamplesMean(int)
,
getEPsamplesStdDev(int)
public final float[][] getListsOfEPsamplesData(int[] midList)
midList
- list of Master Gene Indices to compute expression profilespublic final float[][] getListsOfEPsamplesMean(int[] midList)
midList
- list of Master Gene Indices to compute expression profilespublic final float[][] getListsOfEPsamplesStdDev(int[] midList)
midList
- list of Master Gene Indices to compute expression profilespublic final float[][] getListsOfEPsamplesCV(int[] midList)
midList
- list of Master Gene Indices to compute expression profilespublic final boolean calcOrderedCondListExprProfile(java.lang.String orderedCondListName, int mid)
orderedCondListName
- name of ordered condition list of condition listsmid
- (optionl) Master Gene Index to use in compouting expression profilegetListsOfOrderedCondListMeans()
,
getListsOfOrderedCondListStdDevs()
,
getListsOfOrderedCondListCVs()
,
getListsOfOrderedCondListNbrs()
,
getListsOfOrderedCondListNames()
public final java.lang.String getLastorderedCondListName()
public final float[] getListsOfOrderedCondListMeans()
public final float[] getListsOfOrderedCondListStdDevs()
public final float[] getListsOfOrderedCondListCVs()
public final int[] getListsOfOrderedCondListNbrs()
public final java.lang.String[] getListsOfOrderedCondListNames()
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