Read a data file describing the probe sequences on an Affymetrix genechip
Read a data file describing the probe sequences on an Affymetrix genechip
getProbeDataAffy(arraytype, datafile, pkgname = NULL, comparewithcdf = FALSE)
arraytype |
Character. Array type (e.g. 'HG-U133A') |
datafile |
Character with the filename of the input data file,
or a connection (see example).
If omitted a default name is constructed from |
pkgname |
Character. Package name. If NULL the name is derived
from |
comparewithcdf |
Logical. If TRUE, run a consistency check against a CDF package of the same name (what used to be Laurent's "extraparanoia".) |
This function serves as an interface between
the (1) representation of array probe information data in the packages
that are generated by makeProbePackage and (2) the
vendor- and possibly version-specific way the data are represented
in datafile.
datafile is a tabulator-separated file with one row per probe,
and column names 'Probe X', 'Probe Y',
'Probe Sequence', and 'Probe.Set.Name'. See the vignette
for an example.
A list with three components
dataEnv |
an environment which contains the data frame with the probe sequences and the other probe data. |
symVal |
a named list of symbol value substitutions which can
be used to customize the man pages. See
|
pkgname |
a character with the package name; will be the same
as the function parameter |
makeProbePackage
## Please refer to the vignette
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