AffymetrixProbeTabFile {aroma.affymetrix}R Documentation

The AffymetrixProbeTabFile class

Description

Package: aroma.affymetrix
Class AffymetrixProbeTabFile

Object
~~|
~~+--GenericDataFile
~~~~~~~|
~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--TabularTextFile
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--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 -
fromCdf -
getCdf -
getChipType -
getColumnNames -
getData -
translateFullName -

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

Methods inherited from TabularTextFile:
as.character, getColumnNames, getHeader, getReadArguments, hasColumnHeader, nbrOfLines, nbrOfRows, readColumnNames, readColumns, readDataFrame, readLines, readRawHeader, writeColumnsToFiles

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, getFilename, getFileSize, getFileType, getFullName, getFullNameTranslator, getLastAccessedOn, getLastModifiedOn, getName, getPath, getPathname, getTags, gunzip, gzip, hasBeenModified, hasTag, hasTags, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setFullName, setFullNameTranslator, setName, testAttributes, validateChecksum, writeChecksum

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

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

Author(s)

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


[Package aroma.affymetrix version 1.2.0 Index]