rbamtools: Read and Write BAM (Binary Alignment) Files

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

Author
Wolfgang Kaisers
Date of publication
2016-05-29 15:05:36
Maintainer
Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
License
Artistic-2.0
Version
2.16.0

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