| Package | Description |
|---|---|
| umcg.genetica.io.binInteraction |
| Modifier and Type | Method and Description |
|---|---|
void |
BinaryInteractionFileCreator.addTestedInteraction(String variantName,
String geneName,
String[] covariateNames) |
void |
BinaryInteractionFileCreator.addTestedVariantGene(String variantName,
String geneName) |
boolean |
BinaryInteractionFile.containsInteraction(String variantName,
String geneName,
String covariateName) |
BinaryInteractionFile |
BinaryInteractionFileCreator.create() |
BinaryInteractionFile |
BinaryInteractionFileConstructorBuilder.createBinaryInteractionFile() |
void |
BinaryInteractionFile.finalizeWriting() |
BinaryInteractionGene |
BinaryInteractionFile.getGene(int pointer) |
BinaryInteractionGene |
BinaryInteractionFile.getGene(String name) |
BinaryInteractionVariant |
BinaryInteractionFile.getVariant(int pointer) |
BinaryInteractionVariant |
BinaryInteractionFile.getVariant(String name) |
static BinaryInteractionFile |
BinaryInteractionFile.load(File interactionFile) |
static BinaryInteractionFile |
BinaryInteractionFile.load(File interactionFile,
boolean readOnly) |
protected BinaryInteractionZscores |
BinaryInteractionFile.readInteractionResults(long interactionPointer) |
BinaryInteractionZscores |
BinaryInteractionFile.readInteractionResults(String variantName,
String geneName,
String covariateName) |
BinaryInteractionQtlZscores |
BinaryInteractionFile.readQtlResults(String variantName,
String geneName) |
BinaryInteractionQueryResult |
BinaryInteractionFile.readVariantGeneCovariateResults(String variantName,
String geneName,
String covariateName) |
Iterator<BinaryInteractionQueryResult> |
BinaryInteractionFile.readVariantGeneResults(String variantName,
String geneName) |
void |
BinaryInteractionFile.setInteractionResults(String variantName,
String geneName,
String covariateName,
BinaryInteractionZscores zscores) |
void |
BinaryInteractionFile.setQtlResults(String variantName,
String geneName,
BinaryInteractionQtlZscores zscores) |
| Constructor and Description |
|---|
BinaryInteractionFile(File interactionFile,
boolean readOnly,
BinaryInteractionCohort[] cohorts,
BinaryInteractionGene[] genes,
BinaryInteractionVariant[] variants,
String[] covariates,
int[][] covariatesTested,
long timeStamp,
boolean allCovariants,
boolean metaAnalysis,
boolean normalQtlStored,
boolean flippedZscoreStored,
String fileDescription,
long interactions,
long startQtlBlock,
long startInteractionBlock) |
BinaryInteractionFileCreator(File file,
BinaryInteractionVariantCreator[] variants,
BinaryInteractionGeneCreator[] genes,
BinaryInteractionCohort[] cohorts,
String[] covariates,
boolean allCovariants,
boolean metaAnalysis,
boolean normalQtlStored,
boolean flippedZscoreStored) |
BinaryInteractionQtlZscores(double[] zscores,
int[] sampleCounts) |
BinaryInteractionQtlZscores(double[] zscores,
int[] sampleCounts,
double metaZscore) |
BinaryInteractionQtlZscores(double zscore,
int sampleCounts) |
BinaryInteractionZscores(int[] samplesInteractionCohort,
double[] zscoreSnpCohort,
double[] zscoreCovariateCohort,
double[] zscoreInteractionCohort,
double[] rSquaredCohort) |
BinaryInteractionZscores(int[] samplesInteractionCohort,
double[] zscoreSnpCohort,
double[] zscoreCovariateCohort,
double[] zscoreInteractionCohort,
double[] rSquaredCohort,
double[] zscoreInteractionFlippedCohort) |
BinaryInteractionZscores(int[] samplesInteractionCohort,
double[] zscoreSnpCohort,
double[] zscoreCovariateCohort,
double[] zscoreInteractionCohort,
double[] rSquaredCohort,
double[] zscoreInteractionFlippedCohort,
double zscoreSnpMeta,
double zscoreCovariateMeta,
double zscoreInteractionMeta,
double zscoreInteractionFlippedMeta) |
BinaryInteractionZscores(int[] samplesInteractionCohort,
double[] zscoreSnpCohort,
double[] zscoreCovariateCohort,
double[] zscoreInteractionCohort,
double[] rSquaredCohort,
double zscoreSnpMeta,
double zscoreCovariateMeta,
double zscoreInteractionMeta) |
BinaryInteractionZscores(int samplesInteractionCohort,
double zscoreSnpCohort,
double zscoreCovariateCohort,
double zscoreInteractionCohort,
double rSquaredCohort,
double zscoreInteractionFlippedCohort) |
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