RtaIntensity {ShortRead} | R Documentation

## (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>

### 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")

[Package ShortRead version 1.50.0 Index]