Man pages for Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

applyPileupsApply a user-provided function to calculate pile-up...
ApplyPileupsParam-classParameters for creating pileups from BAM files
BamFile-classMaintain and use BAM files
BamViews-classViews into a set of BAM files
BcfFile-classManipulate BCF files.
defunctRsamtools Deprecated and Defunct
deprecatedDeprecated functions
FaFile-classManipulate indexed fasta files.
headerTabixRetrieve sequence names defined in a tabix file.
indexTabixCompress and index tabix-compatible files.
pileupUse filters and output formats to calculate pile-up...
PileupFiles-classRepresent BAM files for pileup summaries.
quickBamFlagSummaryGroup the records of a BAM file based on their flag bits and...
readPileupImport samtools 'pileup' files.
RsamtoolsFile-classA base class for managing file references in Rsamtools
RsamtoolsFileList-classA base class for managing lists of Rsamtools file references
Rsamtools-package'samtools' aligned sequence utilities interface
scanBamImport, count, index, filter, sort, and merge 'BAM' (binary...
ScanBamParam-classParameters for scanning BAM files
scanBcfOperations on 'BCF' files.
ScanBcfParam-classParameters for scanning BCF files
scanFaOperations on indexed 'fasta' files.
scanTabixOperations on 'tabix' (indexed, tab-delimited) files.
seqnamesTabixRetrieve sequence names defined in a tabix file.
TabixFile-classManipulate tabix indexed tab-delimited files.
testPairedEndBamQuickly test if a BAM file has paired end reads
zipFile compression for tabix (bgzip) and fasta (razip) files.
Rsamtools documentation built on Nov. 17, 2017, 1:55 p.m.