AlignedRead {ShortRead} | R Documentation |
This function constructs objects of
AlignedRead
. It will often be more convenient to
create AlignedRead
objects using parsers such as
readAligned
.
AlignedRead(sread, id, quality, chromosome, position, strand, alignQuality, alignData = AlignedDataFrame(nrow = length(sread)))
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. |
An object of class AlignedRead
.
Martin Morgan <mtmorgan@fhcrc.org>