Package: aroma.affymetrix
Class AffymetrixProbeTabFile
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--TabularTextFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixProbeTabFile
Directly known subclasses:
public abstract static class AffymetrixProbeTabFile
extends AromaPlatformInterface
An AffymetrixProbeTabFile represents an interface to query the data
contained in an Affymetrix probe tab file, e.g.
Mapping250K_Nsp_probe_tab.
AffymetrixProbeTabFile(...)
Arguments passed to the constructor of AffymetrixFile.
Methods:
byChipType | - | |
getCdf | - | |
getChipType | - | |
getColumnNames | - | |
getData | - |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from TabularTextFile:
as.character, getCommentChar, getDefaultColumnClassPatterns, getDefaultColumnClasses, getDefaultColumnNames, getHeader, getReadArguments, hasColumnHeader, nbrOfLines, nbrOfRows, readColumnNames, readColumns, readDataFrame, readLines, readRawHeader, setCommentChar
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Probe-tab files are provided by Affymetrix and contains information on the probes. Note that not necessarily all probes are represented in the files, e.g. typically only PM probes are given and MM are left to be inferred from the PMs.
The below is an extract of the Mapping250K_Nsp_probe_tab file
obtained from the Affymetrix website. Note that columns are separated
by TABs.
SNP_A-1780270 1633 2398 3 TTGTTAAGCAAGTGAGTTATTTTAT f PM C
SNP_A-1780270 1633 2399 3 TTGTTAAGCAAGTGACTTATTTTAT f PM G
SNP_A-1780270 1951 1780 -4 GGATAAAATAAAATAACTCACTTGC r PM C
...
SNP_A-4241299 2553 1658 4 AAACACATTTTTGGGTCGTAAGGAA f PM G
Henrik Bengtsson