DChipSnpInformation: The DChipSnpInformation class
Description
Package: aroma.affymetrix
Class DChipSnpInformation
Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--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(...)
Fields and Methods
Methods:
rll{
byChipType Defines a DChipSnpInformation object by chip type.
readDataFrame -
}
Methods inherited from SnpInformation:
byChipType, fromCdf, fromDataSet, getChipType, getData, getFields, getFragmentLengths, getFragmentStarts, getFragmentStops, isCompatibleWithCdf, nbrOfEnzymes, nbrOfUnits, readDataFrame
Methods inherited from GenericDataFile:
getParentName, compareChecksum, copyTo, equals, fromFile, getAlias, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAlias, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, saveDetails
The dChip SNP information files for various chip types can be
downloaded from http://www.dchip.org/. 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.