AlignedRead {ShortRead} | R Documentation

## (Legacy) 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 1.45.4 Index]