bamAlign-class | R Documentation |
"bamAlign"
The bamAlign class represents the content of a single alignment stored in a BAM-file. An instance of this class can be created by reading an Alignment from an object of class bamReader or bamRange. Accessor functions allow reading and writing of object contents. The alignment can be rewritten to a BAM-file via a bamWriter object or stored in a bamRange object.
Objects can be created by calls of the form new("bamAlign", alignment)
.
align
:Object of class "externalptr"
signature(object = "bamAlign")
: Returns quality scores of aligned read (one for each query-base). Will be reverse of raw if aligned to reverse strand.
signature(object = "bamAlign")
: Returns base sequence of the aligned read. Will be reverse complement of raw if aligned to reverse strand.
signature(object = "bamAlign")
: Returns quality scores of raw read prior to alignment (one for each query-base).
signature(object = "bamAlign")
: Returns base sequence of raw read prior to alignment.
signature(object = "bamAlign")
: Returns data.frame with listed cigar items.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Retrieves 16-bit flag values which contains information of all flags in binary form.
signature(object = "bamAlign")
: Sets 16-bit flag value (all flags at once).
signature(object = "bamAlign", tag="character")
: Retrieves the value of the given tag as a character string, or "" if 'tag' not found.
signature(object = "bamAlign", sep="character")
: Retrieves the complete descriptors of all tags as a character string, with with 'sep' inserted between tags.
signature(.Object = "bamAlign")
: Initializes bamAlign object
signature(object = "bamAlign")
: Returns insertSize value.
signature(object = "bamAlign")
: Returns mapQuality value.
signature(object = "bamAlign")
: Returns mate Position value.
signature(object = "bamAlign")
: Returns mateRefID value.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Returns align read Identifier.
signature(object = "bamAlign")
: Returns number of cigar items in align.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Returns align position (on Ref-Sequence).
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Returns (0-based) ID of Reference Sequence (As indicated by ID column returned by getRefData).
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
signature(object = "bamAlign")
: Gets flag item.
signature(object = "bamAlign")
: Sets flag item.
Wolfgang Kaisers
The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.
http://www.samtools.sourceforge.net/SAM1.pdf
library(rbamtools)
# retrieve align from file
bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam)
align<-getNextAlign(reader)
bamClose(reader)
# use some accessors
readID(align)
refID(align)
position(align)
nCigar(align)
cigarData(align)
alignSeq(align)
alignQual(align)
reverseStrand(align)
reverseStrand(align)<-TRUE
reverseStrand(align)
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