SolexaIntensity {ShortRead} | R Documentation

## (Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"

### Description

These function constructs objects of `SolexaIntensity` and `SolexaIntensityInfo`. It will often be more convenient to create these objects using parsers such as `readIntensities`.

### Usage

    SolexaIntensity(intensity=array(0, c(0, 0, 0)),
                    measurementError=array(0, c(0, 0, 0)),
                    readInfo=SolexaIntensityInfo(
                      lane=integer(nrow(intensity))),
                    ...)
    SolexaIntensityInfo(lane=integer(0),
                        tile=integer(0)[seq_along(lane)],
                        x=integer(0)[seq_along(lane)],
                        y=integer(0)[seq_along(lane)])

### 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 `SolexaIntensityInfo`.
`lane` | An integer vector giving the lane from which each read is derived.
`tile` | An integer vector giving the tile from which each read is derived.
`x` | An integer vector giving the tile-local x coordinate of the read from which each read is derived.
`y` | An integer vector giving the tile-local y coordinate of the read from which each read is derived.
`...` | Additional arguments, not currently used.

### Value

An object of class `SolexaIntensity`, or `SolexaIntensityInfo`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`SolexaIntensity`.

[Package ShortRead version 1.42.0 Index]