cleancdfname {affy} | R Documentation

## Clean Affymetrix's CDF name

### Description

This function converts Affymetrix's names for CDF files to the names used in the annotation pacakge and in all Bioconductor.

### Usage

    cleancdfname(cdfname, addcdf = TRUE)

### Arguments

`cdfname` | A `character` denoting Affymetrix'x CDF file name
`addcdf` | A `logical`. If `TRUE` it adds the string "cdf" at the end of the cleaned CDF name. This is used to name the `cdfenvs` packages.

### Details

This function takes a CDF filename obtained from an Affymetrix file (from a CEL file for example) and convert it to a convention of ours: all small caps and only alphanumeric characters. The details of the rule can be seen in the code. We observed exceptions that made us create a set of special cases for mapping CEL to CDF. The object `mapCdfName` holds information about these cases. It is a `data.frame` of three elements: the first is the name as found in the CDF file, the second the name in the CEL file and the third the name in bioconductor. (note: `mapCdfName` is created dynamically each time you attach the package by a call to the function `library` from the information in the file `mapCdfName.tab` in the `data` directory of your installation of the package)

### Value

A `character`

### Examples

    cdf.tags <- c("HG_U95Av2", "HG-133A")
    for (i in cdf.tags)
      cat(i, "becomes", cleancdfname(i), "\n")

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