ShortRead: RtaIntensity – R documentation

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RtaIntensity

(Legacy) Construct objects of class "RtaIntensity"

Description

RtaIntensity objects contain Illumina image intensity measures created by the RTA pipeline. It will often be more convenient to create this object using readIntensities.

Usage

RtaIntensity(intensity=array(0, c(0, 0, 0)),
             measurementError=array(0, c(0, 0, 0)),
             readInfo=SolexaIntensityInfo(
               lane=integer()[seq_len(nrow(intensity))]),
             ...)

Arguments

`intensity`	A matrix of image intensity values. Successive columns correspond to nucleotides A, C, G, T; four successive columns correspond to each cycle. Typically, derived from `"_int.txt"` files.
`measurementError`	As `intensity`, but measuring standard error. Usually derived from `"_nse.txt"` files.
`readInfo`	An object of class `AnnotatedDataFrame`, containing information described by `RtaIntensityInfo`.
`...`	Additional arguments, not currently used.

Value

An object of class RtaIntensity.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

Examples

rta <- RtaIntensity(array(runif(60), c(5,4,3)))
intensity(rta)
## subsetting, access, and coercion
as(intensity(rta)[1:2,,], "array")

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release