cleancdfname {affy} | R Documentation |
This function converts Affymetrix's names for CDF files to the names used in the annotation pacakge and in all Bioconductor.
cleancdfname(cdfname, addcdf = TRUE)
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. |
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)
A character
cdf.tags <- c("HG_U95Av2", "HG-133A") for (i in cdf.tags) cat(i, "becomes", cleancdfname(i), "\n")