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. mapCdfName
can
bne loaded using data(mapCdfName)
.
A character
cdf.tags <- c("HG_U95Av2", "HG-133A") for (i in cdf.tags) cat(i, "becomes", cleancdfname(i), "\n")