AlignedRead: (Legacy) Construct objects of class "AlignedRead"

In Bioconductor/ShortRead: FASTQ input and manipulation

(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 <[e-mail]>

See Also

AlignedRead.

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.