Man pages for wokai/rbamtools
An R package for reading and writing BAM (Binary alignment) files.

alignDepth-classClass '"alignDepth"': Alignment depth information from...
as.data.frame-methodsConversion of bamRange or gapList into a data.frame
bamAlignbamAlign
bamAlign-classClass '"bamAlign"': Representation of single genomic...
bamClose-methodsbamClose(bamReader), bamClose(bamWriter): Closing of file...
bamCountbamCount: Counting of CIGAR-OP items
bamCountAllbamCountAll
bamGapList-classClass '"bamGapList"'
bamHeader-classClass '"bamHeader"': Representation of data contained in the...
bamHeaderText-classClass '"bamHeader"': Textual representation of header section...
bamRangebamRange(object, coordinates, complex=FALSE): Function for...
bamRange-classClass '"bamRange"': Representation of genomic alignments in...
bamReaderbamReader: Connection to BAM file for reading access.
bamReader-classClass '"bamReader"': Representation for file connection to...
bamSortbamSort: Creation of a sorted copy of a BAM file.
bamWriterbamWriter: Opening a file connection to a BAM file for...
bamWriter-classClass '"bamWriter"': Representation of a file connection to a...
countNucsCounting nucleotides in 'bamAlign' and 'bamRange'
countTextLinescountTextLines: Counting lines in text files.
createIdxBatchcreateIdxBatch: Creation of index files for multiple BAM...
extractBamRegionsextractBamRegions: Extraction of alignments from given...
extractRangesextractRanges: Extraction of alignments
filename-methodsReading 'filename' from bamReader or bamWriter
gapList-classClass '"gapList"': Representation of genomic alignment gaps.
gapSiteList-classClass '"gapSiteList"': Representation of genomic alignment...
getHeaderText-methods'getHeaderText' Assembling member data into Header-Text
getNextAlign-methods'getNextAlign': Retrieving next align from bamReader or...
getQualDfRead and display Phred qualities from bamRange
getRefDataRetrieve reference sequence from a BAM file as data.frame
getValgetVal(object,members): Retrieving values for given types...
headerLine-classClass '"headerLine"': Representation of header line segment...
headerProgram-classClass '"headerProgram"': Represention of header - program...
headerReadGroup-classClass '"headerReadGroup"': Representation of read - group...
isOpen-methodsisOpen(bamReader), isOpen(bamWriter): Checking for opened...
nucStatsTable nucleotides in whole BAM file(s)
rangeSegCount-classClass '"rangeSegCount"': Represents alignment counts in...
rangeToFastqrangeToFastq: Extract read information from alignments for...
rbamtools-packageReading, writing and manipulating BAM-file format.
readerToFastqreaderToFastq: Extraction of a subset of alignments from a...
readPooledBamGapDfreadPooledBamGapDf: Position data for alignments gaps from...
readPooledBamGapsreadPooledBamGaps: Position data for alignments gaps from...
refSeqDict-classClass '"refSeqDict"': Repesentation of data from reference...
setValsetVal(object,members,values): Setting values for given data...
wokai/rbamtools documentation built on May 28, 2017, 5:12 a.m.