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

Description Usage Arguments Details Value Author(s) See Also

View source: R/createAB.R

Description

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

Usage

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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.


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