R: ExiMiR function for creating an AffyBatch object from other...

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