read.marrayLayout: Create objects of class marrayLayout

In marray: Exploratory analysis for two-color spotted microarray data

Description

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

Usage

read.marrayLayout(fname = 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.

Value

An object of class marrayLayout.

Author(s)

Jean Yang [e-mail]

References

http://www.bioconductor.org/

Examples

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

### 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)

marray documentation built on Nov. 8, 2020, 6:46 p.m.