SolexaIntensity: (Legacy) Construct objects of class "SolexaIntensity" and...
In ShortRead: FASTQ input and manipulation

Description Usage Arguments Value Author(s) See Also

View source: R/methods-SolexaIntensity.R

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

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)])

`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.