AromaUnitGenotypeCallFile {aroma.core}R Documentation

The AromaUnitGenotypeCallFile class

Description

Package: aroma.core
Class AromaUnitGenotypeCallFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitGenotypeCallFile

Directly known subclasses:

public static class AromaUnitGenotypeCallFile
extends AromaUnitCallFile

An AromaUnitGenotypeCallFile is a AromaUnitTabularBinaryFile.

Usage

AromaUnitGenotypeCallFile(...)

Arguments

... Arguments passed to AromaUnitTabularBinaryFile.

Fields and Methods

Methods:
allocate -
extractGenotypeMatrix -
extractGenotypes -
isHeterozygous -
isHomozygous -
updateGenotypes -

Methods inherited from AromaUnitCallFile:
allocate, extractCallArray, extractCalls, extractMatrix, findUnitsTodo

Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getAromaUgpFile, getChipType, getExtensionPattern, getFilenameExtension, getPlatform, isAverageFile, nbrOfUnits, readDataFrame

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile

Methods inherited from AromaTabularBinaryFile:
[, [[, [<-, allocate, as.character, colMeans, colMedians, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getColumnNames, importFrom, lapply, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter

Methods inherited from GenericTabularFile:
as.character, dim, extractMatrix, getColumnNames, getColumnNameTranslator, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, setColumnNameTranslator, translateColumnNames

Methods inherited from GenericDataFile:
compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.core version 1.4.0 Index]