rbamtools (version 2.16.17)

Read and Write BAM (Binary Alignment) Files

Description

Provides an R 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

2.16.17

License

Artistic-2.0

Maintainer

Wolfgang Kaisers

Last Published

November 11th, 2019

Functions in rbamtools (2.16.17)

bamCountAll

bamReader-class

Class "bamReader": Representation for file connection to BAM file for reading access.

bamRange

bamRange(object, coordinates, complex=FALSE): Function for reading of alignments in genomic regions.

extractGeneRegions

Extraction of alignments from given genetic regions and BAM files into a set of output BAM files.

extractBamRegions

extractBamRegions: Extraction of alignments from given (genetic) regions and BAM files into a set of output BAM files..

createIdxBatch

createIdxBatch: Creation of index files for multiple BAM files.

countTextLines

countTextLines: Counting lines in text files.

bamHeaderText-class

Class "bamHeader": Textual representation of header section of BAM files.

bamRange-class

Class "bamRange": Representation of genomic alignments in defined regions.

bamWriter

bamWriter: Opening a file connection to a BAM file for writing access.

getNextAlign-methods

getNextAlign: Retrieving next align from bamReader or bamRange

bamSave

bamSave: Creation of a sorted copy of a BAM file.

gapSiteList-class

Class "gapSiteList": Representation of genomic alignment gap positions.

bamReader

bamReader: Connection to BAM file for reading access.

gapList-class

Class "gapList": Representation of genomic alignment gaps.

bamSort

bamSort: Creation of a sorted copy of a BAM file.

extractRanges

extractRanges: Extraction of alignments

getHeaderText-methods

getHeaderText Assembling member data into Header-Text

geneAlignDepth-class

Class "geneAlignDepth": Align-depth data for single genes on multiple samples (BAM files).

filename-methods

Reading filename from bamReader or bamWriter

countNucs

Counting nucleotides in bamAlign and bamRange

getQualDf

Read and display Phred qualities from bamRange

refSeqDict-class

Class "refSeqDict": Repesentation of data from reference sequence dictionary in BAM file header.

sampleBamFiles-class

Class "sampleBamFiles": Data on multiple BAM files from an experimental setting.

readerToFastq

readerToFastq: Extraction of a subset of alignments from a BAM files into fastq format.

bamWriter-class

Class "bamWriter": Representation of a file connection to a BAM file for writing access.

isOpen-methods

isOpen(bamReader), isOpen(bamWriter): Checking for opened file connection to BAM file.

multSeq

Create combined sequences of sequential numbers.

saveAldData

saveAldData: Save alignment depth plots for single genes

exonAlignDepth-class

Class "exonAlignDepth": Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.

exonLoessModel-class

Class "exonLoessModel": Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.

rangeToFastq

rangeToFastq: Extract read information from alignments for given genomic range as fastq.

groupRatio

Calculates group-wise ratios of alignment depth (AD)

headerLine-class

Class "headerLine": Representation of header line segment of header section for BAM files.

rbamtools-package

Reading, writing and manipulating BAM-file format.

headerProgram-class

Class "headerProgram": Represention of header - program section of BAM header.

headerReadGroup-class

Class "headerReadGroup": Representation of read - group data in header section of BAM files

nucStats

Table nucleotides in whole BAM file(s)

readPooledBamGaps

readPooledBamGaps: Position data for alignments gaps from multiple BAM files.

getVal

getVal(object,members): Retrieving values for given types from an object

readPooledBamGapDf

readPooledBamGapDf: Position data for alignments gaps from multiple BAM files.

getRefData

Retrieve reference sequence from a BAM file as data.frame

segmentize

Segmentation of vector using segment coordinates

rangeSegCount-class

Class "rangeSegCount": Represents alignment counts in segments of genetic regions.

setVal

setVal(object,members,values): Setting values for given data items

alignDepth-class

Class "alignDepth": Alignment depth information from bamRange objects.

GenomePartition-class

Class "GenomePartition": .

bamAlign

as.data.frame-methods

Conversion of bamRange or gapList into a data.frame

bamAlign-class

Class "bamAlign": Representation of single genomic alignments.

bamCount

bamCount: Counting of CIGAR-OP items

bamClose-methods

bamClose(bamReader), bamClose(bamWriter): Closing of file connections.

bamGapList-class

Class "bamGapList"

bamHeader-class

Class "bamHeader": Representation of data contained in the header section of BAM files.