ShortRead: AlignedRead – R documentation

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AlignedRead

(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>

AlignedRead

Description

Usage

Arguments

Value

Author(s)

See Also

ShortRead

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