R: Read a GAL file

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

Examples

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

[Package limma version 3.34.5 Index]