Class FactorValueUtils

java.lang.Object

ubic.gemma.model.expression.experiment.FactorValueUtils

public class FactorValueUtils
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DE_EXCLUDE_URI	URI of TGEMO_00014 DE_Exclude, which marks samples to leave out of a differential expression analysis.
static final String	DE_INCLUDE_URI	URI of TGEMO_00013 DE_Include, which marks samples to keep in a differential expression analysis.

Constructor Summary

Constructors

Constructor	Description
FactorValueUtils()

Method Summary

Modifier and Type	Method	Description
static String	getSummaryString(AbstractFactorValueValueObject fv)
static String	getSummaryString(FactorValue fv)	Produce a summary string for this factor value.
static String	getSummaryString(FactorValue fv, String statementDelimiter)
static String	getSummaryString(FactorValue fv, Characteristic category, String statementDelimiter)
static String	getValue(FactorValue fv, String delimiter)	Produce a value for representing a factor value.
static String[]	getValues(FactorValue fv)
static boolean	isDeExcluded(FactorValue fv)	Check if a factor value marks its samples for exclusion from differential expression analysis.
static boolean	isDeIncludeExcludeMarker(FactorValue fv)	Check if a factor value is one of the two DE_Include/DE_Exclude markers.

Methods inherited from class Object

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

Field Details

DE_INCLUDE_URI

public static final String DE_INCLUDE_URI

URI of TGEMO_00013 DE_Include, which marks samples to keep in a differential expression analysis.

See Also:

• Constant Field Values

DE_EXCLUDE_URI

public static final String DE_EXCLUDE_URI

URI of TGEMO_00014 DE_Exclude, which marks samples to leave out of a differential expression analysis.

See Also:

• Constant Field Values

Constructor Details

FactorValueUtils

public FactorValueUtils()

Method Details

isDeExcluded

public static boolean isDeExcluded(FactorValue fv)

Check if a factor value marks its samples for exclusion from differential expression analysis.

isDeIncludeExcludeMarker

public static boolean isDeIncludeExcludeMarker(FactorValue fv)

Check if a factor value is one of the two DE_Include/DE_Exclude markers.

getValue

@Nullable
public static String getValue(FactorValue fv,
 String delimiter)

Produce a value for representing a factor value.

For continuous factors, this will return the value of the measurement. For categorical factors, this will be the subject (or |-delimited concatenation of subjects) of the statements. If there are no statements, FactorValue.getValue() will be used as a fallback.

This value is suitable for displaying in a flat file format. If you need a human-readable summary of the factor value, consider using getSummaryString(FactorValue) instead.

Parameters:

delimiter - delimiter used when joining multiple values from statements

getValues

public static String[] getValues(FactorValue fv)

getSummaryString

public static String getSummaryString(FactorValue fv)

Produce a summary string for this factor value.

getSummaryString

public static String getSummaryString(FactorValue fv,
 String statementDelimiter)

getSummaryString

public static String getSummaryString(FactorValue fv,
 @Nullable
 Characteristic category,
 String statementDelimiter)

getSummaryString

public static String getSummaryString(AbstractFactorValueValueObject fv)