createUniqueCdf.AffymetrixCdfFile: Creates a unique-cell version of the CDF

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Creates a unique-cell version of the CDF

Description

In some cases, single probes map to multiple genome locations. In cases where you may later want to store a probe estimate (e.g. a probe effect or a residual), you will not be able to store more than one per cell. The unique CDF facilitates this by making the cell indices unique (essentially copying the multimapping probes).

Usage

## S3 method for class 'AffymetrixCdfFile'
createUniqueCdf(this, chipType=getChipType(this), tags="unique", path=NULL, units=NULL,
  ..., ram=NULL, verbose=TRUE)

Arguments

chipType	The chip type of the new CDF.
tags	Tags added to the chip type of the new CDF.
path	The path where to store the new CDF file.
...	Additional arguments passed to writeCdf.
ram	A double saying if more or less units should be converted per chunk. A smaller value uses less memory.
verbose	A logical or Verbose.

Details

Note that the set of units in the "unique" CDF is identical to that of the input CDF. So are the unit groups in each unit. Also the number of cells per unit group is preserved. It is only the cell-index composition of each unit group that changes. The cell indices in the unique CDF are guaranteed to occur only once, whereas this may not be true for the input CDF.

Value

Returns the unique CDF as an AffymetrixCdfFile object.

Author(s)

Mark Robinson

See Also

For more information see AffymetrixCdfFile.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.