marray: read.marrayInfo – R documentation

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read.marrayInfo

Create objects of class marrayInfo

Description

This function creates objects of class marrayInfo. The marrayInfo class is used to store information regarding the target mRNA samples co-hybridized on the arrays or the spotted probe sequences (e.g. data frame of gene names, annotations, and other identifiers).

Usage

read.marrayInfo(fname, info.id=NULL, labels=NULL, notes=fname, sep="\t",skip=0, quote="\"", ...)

Arguments

`fname`	the name of the file that stores information on target samples or probe sequences. This is usually a file obtained from a database.
`info.id`	the column numbers in `fname` that contain the required information.
`labels`	the column number in `fname` which contains the names that the user would like to use to label spots or arrays (e.g. for default titles in `maPlot`.
`notes`	object of class character, vector of explanatory text
`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.
`skip`	the number of lines of the data file to skip before beginning to read data.
`quote`	the set of quoting characters. By default, this is disable by setting ‘quote="\""’.
`...`	further arguments to `scan`.

Value

An object of class marrayInfo.

Author(s)

Jean Yang, yeehwa@stat.berkeley.edu

References

http://www.bioconductor.org/

Examples

datadir <- system.file("swirldata", package="marray")

## Reading target sample information
swirl.samples <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))

## Reading probe sequence information
swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"),
                                info.id=4:5, labels=5, skip=21)

marray

Exploratory analysis for two-color spotted microarray data

v1.68.0

LGPL

Authors

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.

Initial release

2009-08-15