read.marrayRaw {marrayInput} | R Documentation

## Create objects of class "marrayRaw"

### Description

This function reads in cDNA microarray data from a directory and creates objects of class `"marrayRaw"` from spot quantification data files obtained from image analysis software or databases.

### Usage

    read.marrayRaw(fnames, path=".", name.Gf, name.Gb=NULL, name.Rf,
    name.Rb=NULL,name.W=NULL, layout=NULL, gnames=NULL, targets=NULL,
    notes=NULL, skip=0, sep="       ", quote="\"",...)

    read.GenePix(fnames = NULL, path = ".", name.Gf = "F532 Mean",
    name.Gb ="B532 Median", name.Rf = "F635 Mean", name.Rb = "B635 Median",
    name.W =NULL, layout = NULL, gnames = NULL, targets = NULL,
    notes = NULL, skip=0, sep = "   ", quote = "\"", ...)

    read.SMDfnames = NULL, path = ".", name.Gf = "CH1I_MEAN",
                     name.Gb = "CH1B_MEDIAN", name.Rf = "CH2I_MEAN",
                     name.Rb = "CH2B_MEDIAN", name.W = NULL, layout =
                     NULL, gnames = NULL, targets = NULL, notes = NULL,
                     skip = 0, sep = "\t", quote = "", ...)

    read.Spot(fnames = NULL, path = ".", name.Gf = "Gmean",
    name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR",
    name.W = NULL, layout = NULL, gnames = NULL, targets = NULL,
    notes = NULL, skip = 0, sep = " ", quote = "\"", ...)

    widget.marrayRawext = c("spot", "xls", "gpr"), skip = 0, sep = "\t",
                     quote = "", ...)

### Arguments

`fnames` | a vector of character strings containing the file names of each spot quantification data file. These typically end in `.spot` for the software `Spot` or `.gpr` for the software `GenePix`.
`path` | a character string representing the data directory. By default this is set to the current working directory ("."). In the case where `fnames` contains the full path name, path should be set to NULL.
`name.Gf` | character string for the column header for green foreground intensities.
`name.Gb` | character string for the column header for green background intensities.
`name.Rf` | character string for the column header for red foreground intensities.
`name.Rb` | character string for the column header for red background intensities.
`name.W` | character string for the column header for spot quality weights.
`layout` | object of class `"marrayLayout"`, containing microarray layout parameters.
`gnames` | object of class `"marrayInfo"` containing probe sequence information.
`targets` | object of class `"marrayInfo"` containing target sample information.
`notes` | object of class `"character"`, vector of explanatory text.
`skip` | the number of lines of the data file to skip before beginning to read in data.
`sep` | the field separator character. Values on each line of the file are separated by this character. The default is to read a tab delimited file.
`quote` | the set of quoting characters. By default, this is disabled by setting `quote="\""`.
`...` | further arguments to `scan`.

### Details

### Value

An object of class `"marrayRaw"`.

### Author(s)

Jean Yang, yeehwa@stat.berkeley.edu

### References

http://www.bioconductor.org/.

### See Also

`scan`, `read.marrayLayout`, `read.marrayInfo`

### Examples

    datadir <- system.file("data", package="marrayInput")

    skip <-  grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1

    swirl.layout <- read.marrayLayout(ngr=4, ngc=4, nsr=22, nsc=24)

    swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))

    swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"),
                                    info.id=4:5, labels=5, skip=skip)

    x <-  maInfo(swirl.gnames)[,1]
    y <- rep(0, maNspots(swirl.layout))
    y[x == "control"] <- 1
    slot(swirl.layout, "maControls") <- as.factor(y)

    fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\."))
    swirl<- read.Spot(fnames, path=datadir,
                           layout = swirl.layout,
                           gnames = swirl.gnames,
                           targets = swirl.targets)

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