public class ClassScoreSimple extends Object
Constructor and Description |
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ClassScoreSimple(List<String> probes,
List<String> genes,
List<Collection<String>> goAssociations)
Note that these Lists must all be in the same order with respect to the probes.
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Modifier and Type | Method and Description |
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double |
getGeneSetPvalue(String id)
Gene the resulting gene set pvalue for a given id.
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void |
run(List<Double> geneScores)
Run an analysis using the current configuration.
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void |
setBigGeneScoreIsBetter(boolean b)
Indicate that in the original gene scores, whether big values are better.
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void |
setClassScoreMethod(int val)
Set the type of anlaysis to run.
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void |
setGeneReplicateTreatment(int val)
How to handle situations when more than one probe corresponds to the same gene.
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void |
setGeneScoreSummaryMethod(int val)
Set the method to be used to summarize gene sets during resampling analysis.
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void |
setGeneScoreThreshold(double val)
Set the threshold to use for ORA analysis.
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void |
setIterations(int val)
The number of iterations to be used during resampling.
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void |
setLogTransformGeneScores(boolean val)
Set to true if your inputs are p-values.
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void |
setMaxGeneSetSize(int val)
The maximum gene set size to be considered.
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void |
setMinGeneSetSize(int val)
The minimum gene set size to be considered.
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public ClassScoreSimple(List<String> probes, List<String> genes, List<Collection<String>> goAssociations)
probes
- List of identifiers to be analyzedgenes
- List of genes corresponding to the probes. Indicates the Many-to-one mapping of probes to genes.goAssociations
- List of Collections of go terms for the probes.public double getGeneSetPvalue(String id)
id
- The id of the gene set, e.g,. GO:0000232public void setBigGeneScoreIsBetter(boolean b)
b
- public void setClassScoreMethod(int val)
val
- either ClassScoreSimple.ORA or ClassScoreSimple.RESAMPLING or ROCpublic void setGeneReplicateTreatment(int val)
val
- either BEST_GENE_SCORE or MEAN_GENE_SCOREpublic void setGeneScoreSummaryMethod(int val)
val
- Either GeneScoreMethod.MEAN, MEDIAN, MEAN_ABOVE_QUANTILE or PRECISIONRECALLpublic void setGeneScoreThreshold(double val)
val
- public void setIterations(int val)
val
- public void setLogTransformGeneScores(boolean val)
val
- If true, your gene scores will be transformed by -log base 10.public void setMaxGeneSetSize(int val)
val
- public void setMinGeneSetSize(int val)
val
- Copyright © 2002-2013 UBC Centre for High-Throughput Biology. All Rights Reserved.