readGAL {limma} | R Documentation

## Read a GAL file

### Description

Read a GenePix Array List (GAL) file into a dataframe.

### Usage

    readGAL(galfile=NULL,path=NULL,header=TRUE,sep="\t",quote="\"",skip=NULL,as.is=TRUE,...)

### Arguments

`galfile` | character string giving the name of the GAL file. If `NULL` then a file with extension `.gal` is found in the directory specified by `path`.
`path` | character string giving the directory containing the files. If `NULL` then assumed to be the current working directory.
`header` | logical variable, if `TRUE` then the first line after `skip` is assumed to contain column headings. If `FALSE` then a value should specified for `skip`.
`sep` | the field separator character
`quote` | the set of quoting characters
`skip` | number of lines of the GAL file to skip before reading data. If `NULL` then this number is determined by searching the file for column headings.
`as.is` | logical variable, if `TRUE` then read in character columns as vectors rather than factors.
`...` | any other arguments are passed to `read.table`

### Details

A GAL file is a list of genes IDs and associated information produced by an Axon microarray scanner. Apart from header information, the file must contain data columns labeled `Block`, `Column`, `Row` and `ID`. A `Name` column is usually included as well. Other columns are optional. See the Axon URL below for a detaile description of the GAL file format.

This function reads in the data columns with a minimum of user information. In most cases the function can be used without specifying any of the arguments.

### Value

A data frame with columns

`Block` | numeric vector containing the print tip indices
`Column` | numeric vector containing the spot columns
`Row` | numeric vector containing the spot rows
`ID` | character vector, for factor if `as.is=FALSE`, containing gene library identifiers
`Name` | character vector, for factor if `as.is=FALSE`, containing gene names

The data frame will be sorted so that `Column` is the fastest moving index, then `Row`, then `Block`.

### Author(s)

Gordon Smyth

### References

http://www.cryer.co.uk/file-types/a/atf/genepix_file_formats.htm

### See Also

`read.Galfile` in the marray package.

An overview of LIMMA functions for reading data is given in 03.ReadingData.

### Examples

    # readGAL()
    # will read in the first GAL file (with suffix ".gal")
    # found in the current working directory

[Package limma version 3.42.2 Index]