ubic.erminej.data

Class GeneScores

java.lang.Object

ubic.erminej.data.GeneScores

public class GeneScores
extends Object

Parse and store probe->score associations. The values are stored in a Map probeToPvalMap. This is used to see what probes are int the data set, as well as the score for each probe.

Version:

$Id: GeneScores.java,v 1.39 2013/05/20 05:06:11 paul Exp $

Author:

Shahmil Merchant, Paul Pavlidis

Constructor Summary

Constructors

Constructor and Description
GeneScores(Collection<String> identifiers, Settings settings, StatusViewer m, GeneAnnotations geneAnnotations, String outputFileName) Constructor for the case when we are just taking in a hit list.
GeneScores(GeneScores source, GeneAnnotations geneAnnots) Create a copy of source that contains only the probes given.
GeneScores(InputStream is, SettingsHolder settings, StatusViewer m, GeneAnnotations geneAnnotations)
GeneScores(List<String> probes, List<Double> scores, GeneAnnotations geneAnnots, SettingsHolder settings) Constructor designed for use when input is not a file.
GeneScores(String filename, SettingsHolder settings, StatusViewer messenger, GeneAnnotations geneAnnots)

Method Summary

Methods

Modifier and Type	Method and Description
Double[]	getGeneScores() Note that these will already be log-transformed, if that was requested by the user.
Double[]	getGeneSetScores(GeneSetTerm geneSetTerm) Get the gene scores for just the genes in the set indicated.
Map<Gene,Double>	getGeneToScoreMap() Note that these values will already be log tranformed if that was requested.
Map<Gene,Double>	getGeneToScoreMap(boolean shuffle)
int	getNumGenesUsed()
int	getNumProbesUsed()
Double[]	getProbeScores() Note that these values will already be log-transformed if that was requested.
Map<Probe,Double>	getProbeToScoreMap() Note that these values will already be log-transformed if that was requested
GeneAnnotations	getPrunedGeneAnnotations()
List<Gene>	getRankedGenes()
String	getScoreColumnName() Might not be available.
double	getValueMap(String probe_id)
boolean	isNegativeLog10Transformed()
int	numGenesAboveThreshold(double geneScoreThreshold)
boolean	rankLargeScoresBest()
String	toString()
void	write(File f) Write the gene scores to a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneScores

public GeneScores(Collection<String> identifiers,
          Settings settings,
          StatusViewer m,
          GeneAnnotations geneAnnotations,
          String outputFileName)

Constructor for the case when we are just taking in a hit list. The scores for all non-hit genes are set such that the appropriate threshold will be zero. Note that no background set can be defined!

Parameters:

identifiers -

settings -

m -

geneAnnotations -

outputFileName - if provided, also save this, and update the settings.

GeneScores

public GeneScores(GeneScores source,
          GeneAnnotations geneAnnots)

Create a copy of source that contains only the probes given.

Parameters:

source -

geneAnnots - - the original gene annotation set, the probes here will be used as a starting point

GeneScores

public GeneScores(InputStream is,
          SettingsHolder settings,
          StatusViewer m,
          GeneAnnotations geneAnnotations)
           throws IOException

Parameters:

is - - input stream

settings -

messenger -

geneAnnotations - Source (original) geneannotation set.

Throws:

IOException

GeneScores

public GeneScores(List<String> probes,
          List<Double> scores,
          GeneAnnotations geneAnnots,
          SettingsHolder settings)

Constructor designed for use when input is not a file.

Parameters:

probes - List of Strings.

scores - List of java.lang.Doubles containing the scores for each probe.

geneAnnots - Source (original) geneannotation set.

settings -

GeneScores

public GeneScores(String filename,
          SettingsHolder settings,
          StatusViewer messenger,
          GeneAnnotations geneAnnots)
           throws IOException

Parameters:

filename -

settings -

messenger -

geneAnnots - Source (original) geneannotation set.

Throws:

IOException

Method Detail

getGeneScores

public Double[] getGeneScores()

Note that these will already be log-transformed, if that was requested by the user.

Returns:

getGeneSetScores

public Double[] getGeneSetScores(GeneSetTerm geneSetTerm)

Get the gene scores for just the genes in the set indicated.

Parameters:

geneSetTerm -

Returns:

getGeneToScoreMap

public Map<Gene,Double> getGeneToScoreMap()

Note that these values will already be log tranformed if that was requested.

Returns:

getGeneToScoreMap

public Map<Gene,Double> getGeneToScoreMap(boolean shuffle)

Parameters:

shuffle - Whether the map should be scrambled first. If so, then groups are randomly associated with scores, but the actual values are the same. This is used for resampling multiple test correction.

Returns:

Map of groups of genes to scores (which will have been -log-transformed already, if requested)

getNumGenesUsed

public int getNumGenesUsed()

getNumProbesUsed

public int getNumProbesUsed()

getProbeScores

public Double[] getProbeScores()

Note that these values will already be log-transformed if that was requested.

Returns:

getProbeToScoreMap

public Map<Probe,Double> getProbeToScoreMap()

Note that these values will already be log-transformed if that was requested

getPrunedGeneAnnotations

public GeneAnnotations getPrunedGeneAnnotations()

Returns:

getRankedGenes

public List<Gene> getRankedGenes()

Returns:

list of genes in order of their scores, where the first gene is the 'best'. If 'big is better', genes with large scores will be given first. If smaller is better (pvalues) and the data are -log transformed (usual), then the gene that had the smallest pvalue will be first.

getScoreColumnName

public String getScoreColumnName()

Might not be available.

Returns:

getValueMap

public double getValueMap(String probe_id)

Parameters:

probe_id -

Returns:

isNegativeLog10Transformed

public boolean isNegativeLog10Transformed()

Returns:

true if these scores were transformed via -log_10(x) when they were read in (according to the settings)

numGenesAboveThreshold

public int numGenesAboveThreshold(double geneScoreThreshold)

Parameters:

geneScoreThreshold -

Returns:

rankLargeScoresBest

public boolean rankLargeScoresBest()

Returns:

true if the values returned by methods such as getGeneToScoreMap are returning values which should be treated as "big better". This will be true in the following (common) cases based on the settings the user made:

• The scores were -log transformed, and small values are better (e.g., input probabilities)
• The scores were not -log transformed, and big values were better in the original input.

See Also:

Settings.upperTail(), which does the same thing.

toString

public String toString()

Overrides:

toString in class Object

write

public void write(File f)
           throws IOException

Write the gene scores to a file. Note: does not affect the setting's value of scoreFile.

Parameters:

f - path to write to

Throws:

IOException