SolexaIntensity: (Legacy) Construct objects of class "SolexaIntensity" and...

In ShortRead: FASTQ input and manipulation

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 <[e-mail]>

See Also

SolexaIntensity.

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