Description Usage Arguments Details Value Author(s) See Also Examples
Reads an Affymetrix chip description file (CDF) and creates an environment used as a hash table for the probe set mapping to location.
1 2 3 4 5 | make.cdf.env(filename,
cdf.path = getwd(),
compress = FALSE,
return.env.only = TRUE,
verbose = TRUE)
|
filename |
Character. Filename of the CDF file - without the path prefix! |
cdf.path |
Character. Path to the CDF file. |
compress |
Logical. If |
return.env.only |
Logical. If |
verbose |
Logical. If |
Normally, this function should not be called directly. The
preferred way to handle CDF information is to use
make.cdf.package
to build a package, and to
install it into R. The CDF information can then either be invoked
automatically by the package affy
, or can be loaded manually by
calling, for example, library(hgu133a)
.
Some R installations (typically on Windows) do not offer all the tools that are necessary for package building. In such situations, this function may be called directly. Please see the vignette for details - type:
openVignette("makecdfenv")
Return values:
env
is an environment, used as a hash table.
For every probe set name we have a matrix with 2 columns. The first
column contains the PM locations and the second column the MM
locations. For PM only chips the MM column will have NAs.
syms
is a list that contains chip-specific (i.e., CDF-file
specific) information that can be used in the construction of the help
files for the CDF package.
Depending on the argument return.env.only
,
either the environment, or a list with two elements,
env
and syms
. See details.
Rafael A. Irizarry, Wolfgang Huber
1 2 3 4 5 | env <- make.cdf.env("Hu6800.CDF.gz",
cdf.path=system.file("extdata", package="makecdfenv"),
compress=TRUE)
length(ls(env))
get("U53347_at", env)
|
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