ReadExi: ExiMiR function for reading Exiqon raw data into an AffyBatch...
In ExiMiR: R functions for the normalization of Exiqon miRNA array data

Description Usage Arguments Details Value Warning Author(s) See Also Examples

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

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

`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.

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.

An AffyBatch object containing the raw expression data.

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

Sylvain Gubian, Alain Sewer, PMP SA

make.gal.env, createAB.

# 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')

ExiMiR documentation built on Nov. 8, 2020, 8:26 p.m.