AffymetrixProbeTabFile: The AffymetrixProbeTabFile class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

AffymetrixProbeTabFile

R Documentation

The AffymetrixProbeTabFile class

Description

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.

Usage

AffymetrixProbeTabFile(...)

Arguments

...

Arguments passed to the constructor of AffymetrixFile.

Fields and Methods

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

About probe-tab files

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