readGAL {limma} | R Documentation |
Read a GenePix Array List (GAL) file into a dataframe.
readGAL(galfile=NULL,path=NULL,header=TRUE,sep="\t",quote="\"",skip=NULL,as.is=TRUE,...)
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 |
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.
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
.
Gordon Smyth
http://www.axon.com/gn_GenePix_File_Formats.html
An overview of LIMMA functions for reading data is given in 03.ReadingData.
# readGAL() # will read in the first GAL file (with suffix ".gal") # found in the current working directory