Description Usage Arguments Fields and Methods Author(s) References See Also
Package: aroma.seq
Class BamDataFile
Object
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FullNameInterface
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GenericDataFile
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SequenceContigsInterface
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~~~~~~~~~~~~~~~~~+--
AromaPathnameInterface
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AromaSeqDataFile
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BamDataFile
Directly known subclasses:
public static class BamDataFile
extends AromaSeqDataFile
A BamDataFile object represents a BAM file.
1 |
... |
Arguments passed to |
Methods:
buildIndex | - | |
convertToSam | - | |
countNucleotides | - | |
doQDNAseq | - | |
extractReadStartPositions | - | |
getChipType | - | |
getFlagStat | - | |
getHeader | - | |
getIndexFile | - | |
getIndexStats | - | |
getPlatform | - | |
getReadCounts | - | |
getReadGroup | - | |
getReadGroups | - | |
getSeqLengths | - | |
getTargetLengths | - | |
getTargetNames | - | |
getTargets | - | |
getTotalTargetLength | - | |
hasIndex | - | |
isPaired | - | |
isSorted | - | |
mpileup | - | |
nbrOfMappedReads | - | |
nbrOfReads | - | |
nbrOfTargets | - | |
nbrOfUnmappedReads | - | |
readDataFrame | - | |
readReadPositions | - | |
replaceAllReadGroups | - | |
sort | - | |
sortByName | - | |
sortByPosition | - | |
tview | - | |
Methods inherited from AromaSeqDataFile:
getDefaultFullName, getDefaultSamReadGroup, getSamReadGroup, isCompatibleWith, setSamReadGroup
Methods inherited from AromaPathnameInterface:
directoryStructure, getOrganism
Methods inherited from SequenceContigsInterface:
cleanSeqNames, getSeqGenericSummary, getSeqLengths, getSeqNames, getSeqOrdering, getTotalSeqLength, hasDuplicatedSeqs, hasSeqLengths, isCompatibleWithBySeqLengths, isCompatibleWithBySeqNames, isCompatibleWithBySeqs, nbrOfSeqs
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, directoryItem, directoryItems, directoryStructure, directoryStructure<-, getDataSetName, getOrganismName, getSampleName, loadCacheFile, loadCacheFileItem, memoizedCall2, saveCacheFile, saveCacheFileItem, 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, findRspReportTemplate, asThis
Henrik Bengtsson
[1] The SAM Format Specification Working Group,
The SAM Format Specification, Sept 7, 2011.
An object of this class is typically part of an
BamDataSet
.
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