read.rg: Read RGList\_CALIB from Image Analysis Output Files

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

Reads an RGList\_CALIB from a series of microarray image analysis output files

Usage

read.rg(files = NULL, source = "generic", path = NULL, ext = NULL, 
        names = NULL, columns = NULL, other.columns = NULL,
        annotation = NULL,wt.fun = NULL, verbose = TRUE, sep = "\t",
        quote = NULL, DEBUG = FALSE, ...)

Arguments

files	character vector giving the names of the files containing image analysis output or, for Imagene data, a character matrix of names of files. If omitted, then all files with extension ext in the specified directory will be read in alphabetical order.
source	character string specifying the image analysis program which produced the output files. Choices are "generic", "agilent", "arrayvision", "bluefuse", "genepix", "genepix.custom", "genepix.median", "imagene", "quantarray", "scanarrayexpress", "smd.old", "smd", "spot" or "spot.close.open".
path	character string giving the directory containing the files. The default is the current working directory.
ext	character string giving optional extension to be added to each file name
names	character vector of names to be associated with each array as column name. Defaults to removeExt(files).
columns	list with fields R, G, Rb, Gb, RArea and GArea giving the column names to be used for red foreground, green foreground, red background, green background, red area and green area respectively. Or, in the case of Imagene data, a list with fields f and b. This argument is optional if source is specified, otherwise it is required.
other.columns	character vector of names of other columns to be read containing spot-specific information
annotation	character vector of names of columns containing annotation information about the probes
wt.fun	function to calculate spot quality weights
verbose	logical, TRUE to report each time a file is read
sep	the field separator character
quote	character string of characters to be treated as quote marks
DEBUG	a logical value, if TRUE, a series of echo statements will be printed for each file. Details on the file, skip, and selected columns in a colClasses format for read.table will be displayed.
...	any other arguments are passed to read.table.

Details

This is the main data input function for CALIB package. It has the similar usage as the read.maimages function in limma package. The output of the function is an RGList_CALIB object. However,there are two more fields - $RArea and $GArea than RGList object in limma package. These two fields contain spot area of each color. More details see read.maimages in limma package.

Value

An RGList_CALIB object containing the components

R	matrix containing the red channel foreground intensities for each spot for each array.
G	matrix containing the green channel foreground intensities for each spot for each array.
Rb	matrix containing the red channel background intensities for each spot for each array.
Gb	matrix containing the green channel background intensities for each spot for each array.
RArea	matrix containing the red spot area for each spot for each array.
GArea	matrix containing the green spot area for each spot for each array.
weights	spot quality weights, if wt.fun is given
other	list containing matrices corresponding to other.columns if given
genes	data frame containing annotation information about the probes, for example gene names and IDs and spatial positions on the array, currently set only if source is "agilent", "genepix" or source="imagene" or if the annotation argument is set
targets	data frame with column FileName giving the names of the files read
source	character string giving the image analysis program name
printer	list of class PrintLayout, currently set only if source="imagene"

Author(s)

Hui Zhao

References

read.maimages in limma package

See Also

'read.rg' is based on read.table in the base package

Examples

 #  Read all .gpr files from current working directory.

 # files <- dir(pattern="*\.gpr$")
 # RG <- read.rg(files,"genepix")

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.