R: Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"

SolexaIntensity {ShortRead}

R Documentation

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(length(lane)),
                    x=integer(length(lane)),
                    y=integer(length(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)