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

In ShortRead: FASTQ input and manipulation

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 <[e-mail]>

See Also

RtaIntensity, readIntensities.

Examples

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

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.