AlignedRead {ShortRead} | R Documentation |
Construct objects of class "AlignedRead"
Description
This function constructs objects of
AlignedRead
. It will often be more convenient to
create AlignedRead
objects using parsers such as
readAligned
.
Usage
AlignedRead(sread, id, quality, chromosome, position, strand,
alignQuality,
alignData = AlignedDataFrame(nrow = length(sread)))
Arguments
sread |
An object of class DNAStringSet , containing the
DNA sequences of the short reads.
|
id |
An object of class BStringSet , containing the
identifiers of the short reads. This object is the same length as
sread .
|
quality |
An object of class BStringSet , containing the
ASCII-encoded quality scores of the short reads. This object is the
same length as sread .
|
chromosome |
A factor describing the particular sequence
within a set of target sequences (e.g. chromosomes in a genome
assembly) to which each short read aligns.
|
position |
A integer vector describing the (base pair)
position at which each short read begins its alignment.
|
strand |
A factor describing the strand to which the short
read aligns.
|
alignQuality |
A numeric vector describing the alignment
quality.
|
alignData |
An AlignedDataFrame with number of rows equal
to the length of sread , containing additional information
about alignments.
|
Value
An object of class AlignedRead
.
Author(s)
Martin Morgan <mtmorgan@fhcrc.org>
See Also
AlignedRead
.
[Package
ShortRead version 1.12.4
Index]