DChipSnpInformation: 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.

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, objectSize, print, save, asThis

Details

The dChip SNP information files for various chip types can be downloaded from http://www.hsph.harvard.edu/cli/complab/dchip/. 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.