AromaUnitTotalCnBinaryFile    package:aroma.core    R Documentation

_T_h_e _A_r_o_m_a_U_n_i_t_T_o_t_a_l_C_n_B_i_n_a_r_y_F_i_l_e _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     Package:  aroma.core 
      *Class AromaUnitTotalCnBinaryFile*

     'Object'
      '~~|'
      '~~+--''FullNameInterface'
      '~~~~~~~|'
      '~~~~~~~+--''GenericDataFile'
      '~~~~~~~~~~~~|'
      '~~~~~~~~~~~~+--''GenericTabularFile'
      '~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~+--''AromaTabularBinaryFile'
      '~~~~~~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~~~~~~+--''AromaPlatformInterface'
      '~~~~~~~~~~~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~~~~~~~~~~~+--''AromaUnitSignalBinaryFile'
      '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|'
      '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--''CopyNumberDataFile'
      '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|'

     '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--''AromaUnitTotalCnBinaryFile'

     *Directly known subclasses:*


     public static class *AromaUnitTotalCnBinaryFile*
      extends _CopyNumberDataFile_

     An AromaUnitTotalCnBinaryFile is a 'AromaUnitSignalBinaryFile'.

_U_s_a_g_e:

     AromaUnitTotalCnBinaryFile(...)

_A_r_g_u_m_e_n_t_s:

     ...: Arguments passed to 'AromaUnitSignalBinaryFile'.

_F_i_e_l_d_s _a_n_d _M_e_t_h_o_d_s:

     *Methods:*

         'extractRawCopyNumbers'     -
         'getAM'                     -
         'getNumberOfFilesAveraged'  -
         'getXAM'                    -
         'hasAlleleBFractions'       -
         'hasStrandiness'            -

     *Methods inherited from CopyNumberDataFile*:
      as, as.CopyNumberDataFile, getNumberOfFilesAveraged,
     hasAlleleBFractions, hasStrandiness

     *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

_A_u_t_h_o_r(_s):

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

