createAB {ExiMiR} | R Documentation

## ExiMiR function for creating an AffyBatch object from other object types (RGList, EListRaw, MAList or list)

### Description

This function creates an `AffyBatch` object from a `limma` object (`RGList`, `EListRaw`, `MAList`) or from any appropriate `list` object.

### Usage

    createAB(object,
             verbose=TRUE,
             ref.channel="R",
             genes.block=NULL,
             genes.row=NULL,
             genes.col=NULL,
             genes.id=NULL,
             genes.name=NULL,
             galname=NULL,
             env.overwrite=TRUE,
             ...)

### Arguments

`object` | An appropriate `EListRaw`, `RGList`, `MAList` or `list` object.
`verbose` | Logical. The default value is `TRUE`. The details of the function execution are displayed on the console.
`genes.block` | Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column in the `object$genes` data frame that contains the block or field values.
`genes.row` | Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column in the `object$genes` data frame that contains the row values.
`genes.col` | Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column in the `object$genes` data frame that contains the column values.
`genes.id` | Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column in the `object$genes` data frame that contains the gene IDs.
`genes.name` | Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column in the `object$genes` data frame that contains gene names.
`ref.channel` | Character vector. The value of the reference channel for two-color arrays ('R' or 'G')
`galname` | Character vector. The default value is `NULL`. In this case the GAL annotation environment used by `createAB` 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 `createAB` or by `make.gal.env`), `galname` allows to force `createAB` to use it for generating the resulting `AffyBatch` object.
`env.overwrite` | Logical. The default value is `TRUE`. If a GAL annotation environment with the same name already exists in the memory, it will be overwritten. This may be useful when the piece of code containing `createAB` is run several times.
`...` | Any additional argument that can be given to the `AffyBatch` constructor, as specified in the documentation of the `AffyBatch` object provided in the `affy` package.

### Details

See accompanying vignette.

### Value

An `AffyBatch` object containing the raw expression data.

### Author(s)

Sylvain Gubian, Alain Sewer, PMP SA

### See Also

`ReadExi`, `make.gal.env`.

[Package ExiMiR version 2.29.1 Index]