rbamtools: Read and Write BAM (Binary Alignment) Files

Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.

AuthorWolfgang Kaisers
Date of publication2016-05-29 15:05:36
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseArtistic-2.0
Version2.16.0

View on CRAN

Man pages

alignDepth-class: Class '"alignDepth"': Alignment depth information from...

as.data.frame-methods: Conversion of bamRange or gapList into a data.frame

bamAlign: bamAlign

bamAlign-class: Class '"bamAlign"': Representation of single genomic...

bamClose-methods: bamClose(bamReader), bamClose(bamWriter): Closing of file...

bamCount: bamCount: Counting of CIGAR-OP items

bamCountAll: bamCountAll

bamGapList-class: Class '"bamGapList"'

bamHeader-class: Class '"bamHeader"': Representation of data contained in the...

bamHeaderText-class: Class '"bamHeader"': Textual representation of header section...

bamRange: bamRange(object, coordinates, complex=FALSE): Function for...

bamRange-class: Class '"bamRange"': Representation of genomic alignments in...

bamReader: bamReader: Connection to BAM file for reading access.

bamReader-class: Class '"bamReader"': Representation for file connection to...

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

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

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

bamWriter-class: Class '"bamWriter"': Representation of a file connection to a...

countNucs: Counting nucleotides in 'bamAlign' and 'bamRange'

countTextLines: countTextLines: Counting lines in text files.

createIdxBatch: createIdxBatch: Creation of index files for multiple BAM...

exonAlignDepth-class: Class '"exonAlignDepth"': Align-depth data for single genes...

exonLoessModel-class: Class '"exonLoessModel"': Align-depth data for single genes...

extractBamRegions: extractBamRegions: Extraction of alignments from given...

extractGeneRegions: Extraction of alignments from given genetic regions and BAM...

extractRanges: extractRanges: Extraction of alignments

filename-methods: Reading 'filename' from bamReader or bamWriter

gapList-class: Class '"gapList"': Representation of genomic alignment gaps.

gapSiteList-class: Class '"gapSiteList"': Representation of genomic alignment...

geneAlignDepth-class: Class '"geneAlignDepth"': Align-depth data for single genes...

GenomePartition-class: Class '"GenomePartition"': .

getHeaderText-methods: 'getHeaderText' Assembling member data into Header-Text

getNextAlign-methods: 'getNextAlign': Retrieving next align from bamReader or...

getQualDf: Read and display Phred qualities from bamRange

getRefData: Retrieve reference sequence from a BAM file as data.frame

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

groupRatio: Calculates group-wise ratios of alignment depth (AD)

headerLine-class: Class '"headerLine"': Representation of header line segment...

headerProgram-class: Class '"headerProgram"': Represention of header - program...

headerReadGroup-class: Class '"headerReadGroup"': Representation of read - group...

isOpen-methods: isOpen(bamReader), isOpen(bamWriter): Checking for opened...

multseq: Create combined sequences of sequential numbers.

nucStats: Table nucleotides in whole BAM file(s)

rangeSegCount-class: Class '"rangeSegCount"': Represents alignment counts in...

rangeToFastq: rangeToFastq: Extract read information from alignments for...

rbamtools-package: Reading, writing and manipulating BAM-file format.

readerToFastq: readerToFastq: Extraction of a subset of alignments from a...

readPooledBamGapDf: readPooledBamGapDf: Position data for alignments gaps from...

readPooledBamGaps: readPooledBamGaps: Position data for alignments gaps from...

refSeqDict-class: Class '"refSeqDict"': Repesentation of data from reference...

sampleBamFiles-class: Class '"sampleBamFiles"': Data on multiple BAM files from an...

saveAldData: saveAldData: Save alignment depth plots for single genes

segmentize: Segmentation of vector using segment coordinates

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

Files in this package

rbamtools
rbamtools/inst
rbamtools/inst/extdata
rbamtools/inst/extdata/accepted_hits.bam.bai
rbamtools/inst/extdata/test.fastq
rbamtools/inst/extdata/accepted_hits.bam
rbamtools/inst/doc
rbamtools/inst/doc/rbamtools.pdf
rbamtools/inst/doc/rbamtools.R
rbamtools/inst/doc/rbamtools.Rnw
rbamtools/tests
rbamtools/tests/test_bam_align.r
rbamtools/tests/test_range_seg_count.r
rbamtools/tests/test_vector_segmentation.r
rbamtools/tests/test_bam_range.r
rbamtools/tests/test_bam_header.r
rbamtools/tests/test_genome_partition.r
rbamtools/tests/test-all.R
rbamtools/src
rbamtools/src/gap_list.h
rbamtools/src/Makevars
rbamtools/src/align_list.h
rbamtools/src/gapSiteList.h
rbamtools/src/grange.h
rbamtools/src/bitmask.h
rbamtools/src/range_partition.h
rbamtools/src/gapSiteListList.h
rbamtools/src/samtools
rbamtools/src/samtools/bam_index.c
rbamtools/src/samtools/bam_endian.h
rbamtools/src/samtools/sam.h
rbamtools/src/samtools/sam_header.c
rbamtools/src/samtools/bam_aux.c
rbamtools/src/samtools/kstring.c
rbamtools/src/samtools/bgzf.c
rbamtools/src/samtools/bgzf.h
rbamtools/src/samtools/ksort.h
rbamtools/src/samtools/bam_import.c
rbamtools/src/samtools/bam_sort.c
rbamtools/src/samtools/bam.c
rbamtools/src/samtools/sam.c
rbamtools/src/samtools/kseq.h
rbamtools/src/samtools/khash.h
rbamtools/src/samtools/faidx.c
rbamtools/src/samtools/razf.c
rbamtools/src/samtools/razf.h
rbamtools/src/samtools/LICENSE
rbamtools/src/samtools/kstring.h
rbamtools/src/samtools/faidx.h
rbamtools/src/samtools/rdef.h
rbamtools/src/samtools/bam.h
rbamtools/src/samtools/sam_header.h
rbamtools/src/rbamtools.h
rbamtools/src/align_counts.h
rbamtools/src/data_frame.h
rbamtools/src/Makevars.win
rbamtools/src/rbamtools.cpp
rbamtools/src/extptr.h
rbamtools/NAMESPACE
rbamtools/NEWS
rbamtools/R
rbamtools/R/segmentize.r
rbamtools/R/rbamtools.r
rbamtools/R/sampleBamFiles.r
rbamtools/vignettes
rbamtools/vignettes/rbamtools.bib
rbamtools/vignettes/rbamtools.Rnw
rbamtools/MD5
rbamtools/build
rbamtools/build/vignette.rds
rbamtools/DESCRIPTION
rbamtools/ChangeLog
rbamtools/man
rbamtools/man/bamCountAll.Rd rbamtools/man/groupRatio.Rd rbamtools/man/countTextLines.Rd rbamtools/man/countNucs.Rd rbamtools/man/getNextAlign-methods.Rd rbamtools/man/rangeSegCount-class.Rd rbamtools/man/rbamtools-package.Rd rbamtools/man/refSeqDict-class.Rd rbamtools/man/createIdxBatch.Rd rbamtools/man/bamClose-methods.Rd rbamtools/man/multseq.Rd rbamtools/man/GenomePartition-class.Rd rbamtools/man/bamSave.Rd rbamtools/man/bamCount.Rd rbamtools/man/geneAlignDepth-class.Rd rbamtools/man/isOpen-methods.Rd rbamtools/man/extractBamRegions.Rd rbamtools/man/getQualDf.Rd rbamtools/man/segmentize.Rd rbamtools/man/headerReadGroup-class.Rd rbamtools/man/readPooledBamGapDf.Rd rbamtools/man/bamHeaderText-class.Rd rbamtools/man/getVal.Rd rbamtools/man/exonAlignDepth-class.Rd rbamtools/man/gapList-class.Rd rbamtools/man/nucStats.Rd rbamtools/man/getHeaderText-methods.Rd rbamtools/man/bamAlign-class.Rd rbamtools/man/readPooledBamGaps.Rd rbamtools/man/headerProgram-class.Rd rbamtools/man/bamSort.Rd rbamtools/man/bamGapList-class.Rd rbamtools/man/alignDepth-class.Rd rbamtools/man/rangeToFastq.Rd rbamtools/man/bamWriter-class.Rd rbamtools/man/gapSiteList-class.Rd rbamtools/man/exonLoessModel-class.Rd rbamtools/man/bamWriter.Rd rbamtools/man/bamRange-class.Rd rbamtools/man/setVal.Rd rbamtools/man/readerToFastq.Rd rbamtools/man/bamReader-class.Rd rbamtools/man/bamAlign.Rd rbamtools/man/bamHeader-class.Rd rbamtools/man/extractGeneRegions.Rd rbamtools/man/extractRanges.Rd rbamtools/man/bamReader.Rd rbamtools/man/getRefData.Rd rbamtools/man/filename-methods.Rd rbamtools/man/saveAldData.Rd rbamtools/man/headerLine-class.Rd rbamtools/man/bamRange.Rd rbamtools/man/as.data.frame-methods.Rd rbamtools/man/sampleBamFiles-class.Rd

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