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

DChipSnpInformation

R Documentation

The DChipSnpInformation class

Description

Package: aroma.affymetrix
Class DChipSnpInformation

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--SnpInformation
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--DChipSnpInformation

Directly known subclasses:

public abstract static class DChipSnpInformation
extends SnpInformation

This class represents dChip genome information files, which typically contains information on nucleotide sequences and fragment lengths of the units.

Usage

DChipSnpInformation(...)

Arguments

...

Arguments passed to SnpInformation.

Details

The dChip SNP information files for various chip types can be downloaded from https://sites.google.com/site/dchipsoft/. Put each file in a directory named identically as the corresponding chip type under the annotations/ directory, e.g. annotations/Mapping50K_Hind240/50k hind snp info AfAm june 05 hg17.xls. Note that dChip changes the filename and file format slightly between chip types, but currently the *byChipType() basically searches for files with names consisting of "snp info" or "snp_info". At least for the most common chip types, there is no need to rename the files in order for this class to recognize them.

Fields and Methods

Methods:

	`byChipType`	-
	`readDataFrame`	-

Methods inherited from SnpInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getData, getFields, getFragmentLengths, getFragmentStarts, getFragmentStops, isCompatibleWithCdf, nbrOfEnzymes, nbrOfUnits, readDataFrame, verify

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

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