CdfEnvAffy-class {altcdfenvs} | R Documentation |
A class to hold the information necessary to handle the grouping of probes in set of probes, and to find XY coordinates of probes on a chip
Objects can be created by calls of the form new("CdfEnvAffy", ...)
.
Typically, there is an instance of the class for each type of chip
(e.g. Hu6800, HG-U95A, etc...).
envir
:"environment"
. It has to
be tought of as a hashtable: the keys are probe set identifiers,
or gene names, and the values are indexes.envName
:"character"
. A name
for the environment.index2xy
:"function"
. The
function used to resolve index into xy coordinates. Unless you are
an advanced user, you probably want to ignore this (and rely on the
default provided with the package).xy2index
:"function"
. The
function used to resolve xy coordinates into index. Unless you are
an advanced user, you probably want to ignore this (and rely on the
default provided with the package).nrow
:"integer"
. The number of
rows of probes for the chip type.ncol
:"integer"
. The number of
columns of probes for the chip type.probeTypes
:"character"
. The
different types of probes stored for each probe set. In the case
of {it Affymetrix} chips, the probes are typically perfect match
(pm) probes or mismatch probes (mm).chipType
:"character"
. The name
of the chip type the instance is associated with. This is useful
when one starts to create alternative mappings of the probes on a
chip (see associated vignette).signature(object = "CdfEnvAffy")
: subset a cdf, that
is return a new cdf containing only a subset of the probe
sets. The subset of probe sets to take is identified as a vector
of identifiers (mode "character").signature(object = "CdfEnvAffy", "environment")
: coerce an
instance of the class to an enviroment
.signature(object = "CdfEnvAffy", "Cdf")
: coerce an
instance of the class to a Cdf
.signature(object="CdfEnvAffy")
: Return the
names of the known probe sets (of course, it depends on the associated CDF).signature(object = "CdfEnvAffy", i="integer")
: convert
index values into XY coordinates.signature(object = "CdfEnvAffy", which =
"character", probeSetNames = NULL)
: obtain the indexes for the probes associated wit
the probe set name probeSetNames
. When probeSetNames
is set to NULL
(default), the indexes are returned for the
probe sets defined on the chip. See indexProbes.CdfEnvAffy
signature(x = "CdfEnvAffy", y = "missing")
: Plot
the chip. It mainly sets coordinates for further plotting (see
examples). See plot.CdfEnvAffy
signature(object = "CdfEnvAffy")
: Print method.signature(object = "CdfEnvAffy", x="integer", y="integer")
: convert XY
coordinates into index values.signature(object = "CdfEnvAffy")
: convert XY
coordinates into index values.Laurent Gautier
indexProbes.CdfEnvAffy
, plot.CdfEnvAffy
## build an instance library(hgu95acdf) cdfenv.hgu95a <- wrapCdfEnvAffy(hgu95acdf, 640, 640, "HG-U95A") show(cdfenv.hgu95a) ## find the indexes for a probe set (pm only) ip <- indexProbes(cdfenv.hgu95a, "pm", "1000_at")[[1]] ## get the XY coordinates for the probe set xy <- index2xy(cdfenv.hgu95a, ip) ## plot the chip plot(cdfenv.hgu95a) ## plot the coordinates plotLocation(xy) ## subset the environment cdfenv.hgu95a.mini <- cdfenv.hgu95a["1000_at"]