Man pages for rbamtools
Read and Write BAM (Binary Alignment) Files
| 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... |
