ReadExi {ExiMiR} | R Documentation

## ExiMiR function for reading Exiqon raw data into an AffyBatch object.

### Description

This function reads Exiqon raw data in ImaGene file format and creates an `AffyBatch` object.

### Usage

    ReadExi(txtfile.path=getwd(),
            galname=NULL,
            description=NULL,
    	notes='',
    	rm.background=FALSE,
    	verbose=TRUE)

### Arguments

`txtfile.path` | Character vector. It contains the path to the folder containing the `samplesinfo.txt` file and the Exiqon raw data files in ImaGene `txt` format.
`galname` | Character vector. The default value is `NULL`. In this case the GAL annotation environment used by `ReadExi` for generating the resulting `AffyBatch` object is lost. Assigning `galname` a non-empty value allows to control this GAL environment, which is useful in two specific situations. First, it gives a handle to this GAL annotation environment for later use. Second, if an adequate GAL annotation environment already exists in the memory (e.g. after having been generated by `ReadExi` or by `make.gal.env`), `galname` allows to force `ReadExi` to use it for generating the resulting `AffyBatch` object.
`description` | Object of class MIAME, as specified in the documentation of the `AffyBatch` object provided in the `affy` package.
`notes` | Character vector, as specified in the documentation of the `AffyBatch` object provided in the `affy` package.
`rm.background` | Logical. This option is kept for compatibility reasons but it is not used anymore. See the `NormiR` options for background correction.
`verbose` | Logical. The default value is `TRUE`. The details of the function execution are displayed on the console.

### Details

The Exiqon miRNA raw expression data are normally in ImageGene `txt` file format and accompanied by a `samplesinfo.txt` description file. It enumerates the names of the sample files for each channel. Therefore the `txtfile.path` argument of `ReadExi` must be a folder that contains the ImageGene and the `samplesinfo.txt` files. If this is not the case, `ReadExi` stops.

The `galname` argument of `ReadExi` must be the name of a GAL annotation environment created with the `make.gal.env` or the `ReadExi` functions. If `galname` is provided a `NULL` value, which is the default situation, a minimal GAL annotation environment is created based on the annotation contained in the ImageGene `txt` files.

### Value

An `AffyBatch` object containing the raw expression data.

### Warning

The `image` method of the `AffyBatch` object might not work properly when the `galname` argument of `ReadExi` has not been assigned.

### Author(s)

Sylvain Gubian, Alain Sewer, PMP SA

### See Also

`make.gal.env`, `createAB`.

### Examples

    # The folder 'Exiqon' contains the file 'samplesinfo.txt' and  the corresponding raw data files in ImaGene format
    ## Not run: ebatch <- ReadExi(txtfile.path='Exiqon')
    # If the GAL environment has already created by the function make.gal.env
    ## Not run: ebatch <- ReadExi(galenv='galenv', txtfile.path='Exiqon')

[Package ExiMiR version 2.28.0 Index]