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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