read.mir: Read in miRNA Data from Agilent Feature Extractiion Output...

In LVSmiRNA: LVS normalization for Agilent miRNA data

Description

Reads intensitity data from a set of one-color microarray image analysis output files.

Usage

                                                                                 
read.mir(files=NULL, source="agilent.median", path=NULL, ext=NULL, names=NULL,
              columns=NULL, other.columns=NULL, annotation=NULL, green.only=TRUE,
              wt.fun=NULL, verbose=TRUE, sep="\t", quote=NULL, remove.ctrl=TRUE,...)

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. Alternatively, it can be a data.frame containing a column called FileName. 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 "agilent.median", "agilent.mean".
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, or named character vector. For two color data, this should have fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background or, in the case of Imagene data, a list with fields f and b. For single channel data, the fields are usually E and Eb. 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
green.only	logical, for use with source, should the green (Cy3) channel only be read, or are both red and green required?. Standard Agilent MIR data have only one channel so defaults to TRUE.
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
remove.ctrl	logical, if TRUE control probes will not be read
...	any other arguments are passed to read.table

Details

This is the main data input function for the LVSmiRNA package for one-color microRNA data. It was originally designed to extract the green channel intensities from a series of files, produced by Agilent Feature Extractiion software, and assembles them into the components of one list. Data from some other image analysis programs can be read if the appropriate column names containing the intensities are specified using the columns argument (This will work if the column names are unique and if there are no incomplete rows in the file after the last line of data. Header lines are ok, if appropriately skipped). The function is a simple wrapper for "read.maimages" in limma package so it shares all its features (though right now the input source is restricted to agilent type file).

The argument files should be a matrix with two columns at least. One column should contain the names of the samples and the other column should contain names of files containing intensity data.

The argument other.columns allows arbitrary columns of the image analysis output files to be reserved in the data object. These become matrices in the 'other' component.

Value

An Elist object.

G	matrix containing the intensities for each array with probes as rows and arrays as columns.
Gb	matrix containing the background intensities for each array with probes as rows and arrays as columns.
targets	data frame with column FileName giving the names of the files read, with column Sample giving the names of the samplse.
genes	data frame containing annotation information about the probes, for examples miRNA names and IDs and positions on the array.
source	character string giving the image analysis program name.
preprocessing	list with components Background, Normalization, is.log, Summarization indicate which pre-processing step has beendone.

Note

All image analysis files being read are assumed to contain data for the same genelist in the same order. No checking is done to confirm that this is true. Probe annotation information is read from one of the files only.

Author(s)

Stefano Calza <[e-mail]>, Suo Chen and Yudi Pawitan.

See Also

read.mir is based on "read.table" in the base package and modified from "read.maimages" in the limma package.

Examples

#  Read all intensity files from current working directory
## Not run: 
dir.files <- system.file("extdata", package="LVSmiRNA")
taqman.data <- read.table(file.path(dir.files,"Comparison_Array.txt"),header=TRUE,as.is=TRUE)
MIR <- read.mir(taqman.data)

## End(Not run)

LVSmiRNA documentation built on Oct. 31, 2019, 5:29 a.m.