The AromaGenomeTextFile class
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.
AromaGenomeTextFile(...)
... |
Arguments passed to |
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.
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:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
# Locate a Human,chromosomes(,.*)*.txt file
db <- AromaGenomeTextFile$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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.