aroma.core (version 3.3.1)

AromaGenomeTextFile: The AromaGenomeTextFile class

Description

Package: aroma.core
Class AromaGenomeTextFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--TabularTextFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaGenomeTextFile

Directly known subclasses:
AromaUcscGenomeTextFile

public abstract static class AromaGenomeTextFile
extends FileCacheKeyInterface

An AromaGenomeTextFile represents a annotation tabular text file that specifies the number of bases (nucleotides) per chromosome for a particular genome/organism.

Usage

AromaGenomeTextFile(...)

Arguments

...

Arguments passed to TabularTextFile.

Fields and Methods

Methods:

	byGenome	-
	readDataFrame	-

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

Author

Henrik Bengtsson

Details

An AromaGenomeTextFile is a tab-delimited text file with a header containing (at least) column names 'chromosome' and 'nbrOfBases'. The 'chromosome' column specifies the chromosomes (character strings) and the 'nbrOfBases' column specifies the lengths (integer) of the chromosomes in number of bases (nucleotides).

The filename of an AromaGenomeTextFile should have format "<genome>,chromosomes(,<tag>)*.txt", and be located in annotationData/genomes/<genome>/, e.g. annotationData/genomes/Human/Human,chromosomes,max,20090503.txt.

Examples

# Locate a Human,chromosomes(,.*)*.txt file
db <- AromaGenomeTextFile$byGenome("Human")
print(db)

# Read the data
df <- readDataFrame(db)
print(df)
str(df)

# Details on the file format
oopts <- options(width=40)
print(readLines(db))
options(oopts)