read.marrayLayout {marrayInput} | R Documentation

## Create objects of class marrayLayout

### Description

This function creates objects of class `marrayLayout` to store layout parameters for two-color cDNA microarrays.

### Usage

    read.marrayLayoutfname = NULL, ngr, ngc, nsr, nsc, pl.col = NULL,
                     ctl.col = NULL, sub.col = NULL, notes = fname, skip,
                     sep = "\t", quote = "\"", ...)

### Arguments

`fname` | the name of the file that stores plate and control information. This is usually a file obtained from a database.
`ngr` | the number of rows of grids per image.
`ngc` | the number of columns of grids per image.
`nsr` | the number of rows of spots per grid.
`nsc` | the number of columns of spots per grid.
`pl.col` | the column number in `fname` that contains plate information.
`ctl.col` | the column number in `fname` that contains control information.
`sub.col` | the column number in `fname` that contains full ID 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 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 disable by setting `quote="""'.
`...` | further arguments to `scan`.

### Details

### Value

An object of class `marrayLayout`.

### Note

### Author(s)

Jean Yang yeehwa@stat.berkeley.edu

### References

http://www.bioconductor.org/

### Examples

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

    ### Reading in control information from file
    skip <-  grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1
    swirl.layout <- read.marrayLayout(fname=file.path(datadir,"fish.gal"), ngr=4, ngc=4,
    nsr=22, nsc=24, ctl.col=4, skip=skip)

    ### Setting control information.
    swirl.gnames <- read.marrayInfo(file.path(datadir,"fish.gal"), info.id=4:5, labels=5, skip=21)
    x <-  maInfo(swirl.gnames)[,1]
    y <- rep(0, maNspots(swirl.layout))
    y[x == "control"] <- 1
    slot(swirl.layout, "maControls") <- as.factor(y)

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