public class FDRUtilities extends Object
Constructor and Description |
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FDRUtilities() |
Modifier and Type | Method and Description |
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static <T extends FDRComputableByDecoys> |
calculateFDR(List<T> items,
String scoreAccession)
Calculate the FDR on the given score sorted List of
FDRComputableByDecoys objects. |
static <T extends FDRComputableByDecoys> |
calculateFDRScore(List<T> items,
String scoreAccession,
boolean oboLookup)
Calculates the FDR score of the report.
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static int |
markDecoys(List<IntermediatePeptideSpectrumMatch> psms,
ProteinAccessionFilter decoysFilter)
This function marks the intermediateProteins of the PSMs, which pass the
given decoysFilter, as decoys for a subsequent FDR estimation.
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public static <T extends FDRComputableByDecoys> void calculateFDR(List<T> items, String scoreAccession)
FDRComputableByDecoys
objects.
The item with the best score must be the first in the list, the worst
score the last.reportItems
- public static <T extends FDRComputableByDecoys> void calculateFDRScore(List<T> items, String scoreAccession, boolean oboLookup)
items
- the list of items, for which the FDR will be calculatedscoreAccession
- the accession of the score used for FDR calculationoboLookup
- whether ob olookup should be performed, if the score is not hard-codedpublic static int markDecoys(List<IntermediatePeptideSpectrumMatch> psms, ProteinAccessionFilter decoysFilter)
psms
- the PSMs, of which the proteins are taggeddecoyFilter
- the filter which specifies the decoysCopyright © 2015. All Rights Reserved.