ShortRead (version 1.30.0)

SolexaIntensity: (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.

See Also

SolexaIntensity.