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rbamtools (version 2.0.1)

Reading, manipulation and writing BAM (Binary alignment) files.

Description

This package provides an interface to functions of the 'SAMtools' C-Library by Heng Li.

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Version

Install

install.packages('rbamtools')

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Version

2.0.1

License

Artistic-2.0

Maintainer

Wolfgang Kaisers

Last Published

March 27th, 2012

Functions in rbamtools (2.0.1)

createIndex

createIndex(bamReader,filename)

bamReader-class

Class "bamReader"

headerReadGroup-class

Class "headerReadGroup"

createIndex-methods

Creating Index file for sorted BAM file

getRefCount-methods

Returns number of reference sequences in BAM file

name-methods

Retrieving read identifier from bamAlign

setVal

setVal(object,members,values)

getHeaderText-methods

getHeaderText Assembling member data into Header-Text

bamRange

bamRange(bamReader, coordinates)

matePosition-methods

Returns position of mate pair align

position-methods

Reads position data member from bamAlign

position

bamAlign accessor functions.

windBack

windBack sets the current align of bamRange before the first align (=past the last align) in the bamRange align list.

filename-methods

Reading filename from bamReader or bamWriter

flag-methods

Reading and writing flag in bamAlign

getPrevAlign-methods

Retrieving previous align from bamRange

writeCurrentAlign-methods

Replaces current align of bamRange with the given bamAlign

reverseStrand-methods

Retrieves strand information from bamAlign

push_back-methods

Appends bamAlign before the first or behind the last element of bamRange

mateReverseStrand-methods

Retrieves or writes value for Strand information of mate pair align

getHeaderText

Reads Header section Text of BAM-file.

getRefData-methods

Retrieving a table with all reference sequences from a bamReader object.

insertPastCurrent-methods

Inserting bamAlign before or past the current Align into bamRange

bamReader

headerProgram-class

Class "headerProgram"

insertSize: Reads insert size from bamAlign

bamSave-methods

Writes bamAligns to an open bamWriter instance

isOpen-methods

isOpen(bamReader),isOpen(bamWriter)

cigarSize-methods

Returns cigar data from bamAlign

paired-methods

Retrieves or writes if align belongs to a paired-end align

writeCurrentAlign

writeCurrentAlign, insertPreCurrent, insert PastCurrent: Writing bamAlign data to bamRange list.

bamSave

bamSave(bamAlign)

mapQuality-methods

Returns quality value for BAM alignment.

bamAlign-class

Class "bamAlign"

windBack-methods

Resets the current align pointer of a bamRange to the position before the first align

refID-methods

Returns refID from bamAlign

filename

filename(bamReader)

firstInPair-methods

Reads or writes information about firstInPair- (secondInPair-) status of bamAlign.

headerLine-class

Class "headerLine"

getNextAlign-methods

getNextAlign: Retrieving next align from bamReader or bamRange

cigarData-methods

Returns (size of) cigar data from bamAlign

getPrevAlign

Reads previous Align from bamRange.

bamRange-class

Class "bamRange"

as.data.frame-methods

Conversion of data stored in bamAlign's in a bamRange into a data.frame

getRefCount

getRefCount: Returns number of reference sequences.

qualities-methods

Retrieves quality string from bamAlign

push_back

Pushing and popping bamAligns on or off a bamRange list.

index.initialized-methods

index.initialized(bamReader)

refSeqDict-class

Class "refSeqDict"

size

Returns size of bamRange list.

readBases-methods

Returns the sequence of nucleobases of the aligned read from a bamAlign

cigarSize

Returns size of cigarData in bamAlign

getVal(object,members)

getRefData

getRefData: Returns an unparsed character string containing the header information of a BAM-file.

flag

Retrieving or setting flagged values of bamAlign objects.

insertSize-methods

Returns value for insertSize from bamAlign

mapQuality

mapQuality: Reads the mapQuality value from bamAlign.

bamClose

bamClose(bamReader), bamClose(bamWriter)

mateUnmapped-methods

Retrieves or writes information about mapping status of mate pair align

matePosition

Read position and reference-ID of mate alignment in paired end reads from a bamAlign.

properPair-methods

Reads or writes the properPair status of bamAlign

unmapped-methods

Reads or writes mapping status of bamAlign

pcrORopt_duplicate-methods

Retrieves or writes if align is PCR or optical duplicate.

mateRefID-methods

Returns refID of mate pair align

isOpen

isOpen(bamReader), isOpen(bamWriter)

bamClose-methods

bamClose(bamReader), bamClose(bamWriter)

pop_front-methods

Removes first (last) bamAlign from bamRange

rbamtools-package

Reading, writing and manipulating BAM-file format.

getNextAlign

Reads next Align from bamReader or bamRange.

secondaryAlign-methods

Reads or writes information about the secondaryAlign status of bamAlign

failedQC-methods

Reading and writing failedQC value in bamAlign