This is a class representation for Affymetrix GeneChip probe
level data. The main component are the intensities from multiple arrays
of the same CDF type. It extends
eSet.
Objects from the Class
Objects can be created using the function read.affybatch
or the wrapper ReadAffy.
Slots
cdfName:
Object of class character representing
the name of CDF file associated with the arrays in the
AffyBatch.
nrow:
Object of class integer representing the
physical number of rows in the arrays.
ncol:
Object of class integer representing the
physical number of columns in the arrays.
assayData:
Object of class AssayData
containing the raw data, which will be at minimum a matrix of
intensity values. This slot can also hold a matrix of standard
errors if the 'sd' argument is set to TRUE in the call to
ReadAffy.
phenoData:
Object of class AnnotatedDataFrame
containing phenotypic data for the samples.
annotation
A character string identifying the
annotation that may be used for the ExpressionSet
instance.
protocolData:
Object of class AnnotatedDataFrame
containing protocol data for the samples.
featureData
Object of class AnnotatedDataFrame
containing feature-level (e.g., probeset-level) information.
experimentData:
Object of class "MIAME" containing
experiment-level information.
.__classVersion__:
Object of class Versions
describing the R and Biobase version number used to create the
instance. Intended for developer use.
Extends
Class "eSet", directly.
Methods
cdfName
signature(object = "AffyBatch"): obtains the
cdfName slot.
pm<-
signature(object = "AffyBatch"): replaces the
perfect match intensities.
pm
signature(object = "AffyBatch"): extracts the pm
intensities.
mm<-
signature(object = "AffyBatch"): replaces the
mismatch intensities.
mm
signature(object = "AffyBatch"): extracts the mm
intensities.
probes
signature(object = "AffyBatch", which): extract
the perfect match or mismatch probe intensities. Uses which can be
"pm" and "mm".
exprs
signature(object = "AffyBatch"): extracts the
expression matrix.
exprs<-
signature(object = "AffyBatch", value = "matrix"):
replaces the expression matrix.
se.exprs
signature(object = "AffyBatch"): extracts the
matrix of standard errors of expression values, if available.
se.exprs<-
signature(object = "AffyBatch", value = "matrix"):
replaces the matrix of standard errors of expression values.
[<-
signature(x = "AffyBatch"): replaces subsets.
[
signature(x = "AffyBatch"): subsets by array.
boxplot
signature(x = "AffyBatch"): creates a
boxplots of log base 2 intensities (pm, mm or both).
Defaults to both.
hist
signature(x = "AffyBatch"): creates a plot showing
all the histograms of the pm,mm or both data. See
plotDensity.
computeExprSet
signature(x = "AffyBatch",
summary.method = "character"): For each probe set computes an
expression value using summary.method.
featureNames
signature(object = "AffyBatch"): return the
probe set names also referred to as the Affymetrix IDs. Notice that
one can not assign featureNames. You must do this by changing
the cdfenvs.
geneNames
signature(object="AffyBatch'"): deprecated,
use featureNames.
getCdfInfo
signature(object = "AffyBatch"): retrieve
the environment that defines the location of probes by probe set.
image
signature(x = "AffyBatch"): creates an image for
each sample.
indexProbes
signature(object = "AffyBatch", which = "character"):
returns a list with locations of the probes in each probe set. The
affyID corresponding to the probe set to retrieve can be specified in
an optional parameter genenames. By default, all the affyIDs
are retrieved. The names of the elements in the list returned are the
affyIDs. which can be "pm", "mm", or "both". If "both" then
perfect match locations are given followed by mismatch locations.
signature(object = "AffyBatch", which = "missing") (i.e.,
calling indexProbes without a "which" argument) is the
same as setting "which" to "pm".
intensity<-
signature(object = "AffyBatch"): a
replacement method for the exprs slot, i.e. the intensities.
intensity
signature(object = "AffyBatch"): extract the
exprs slot, i.e. the intensities.
length
signature(x = "AffyBatch"): returns the number
of samples.
pmindex
signature(object = "AffyBatch"): return the
location of perfect matches in the intensity matrix.
mmindex
signature(object = "AffyBatch"): return the
location of the mismatch intensities.
dim
signature(x = "AffyBatch"): Row and column dimensions.
ncol
signature(x = "AffyBatch"): An accessor function
for ncol.
nrow
signature(x = "AffyBatch"): an accessor function
for nrow.
normalize
signature(object = "AffyBatch"): a method to
normalize. The method accepts an argument
method. The default methods is specified in package options
(see the main vignette).
normalize.methods
signature(object = "AffyBatch"):
returns the normalization methods defined for this class. See
normalize.
probeNames
signature(object = "AffyBatch"): returns
the probe set associated with each row of the intensity matrix.
probeset
signature(object = "AffyBatch",genenames=NULL,
locations=NULL): Extracts ProbeSet
objects related to the probe sets given in genenames. If an alternative
set of locations defining pms and mms a list with those locations should
be passed via the locations argument.
bg.correct
signature(object = "AffyBatch",
method="character") applies background correction methods defined by
method.
updateObject
signature(object = "AffyBatch", ...,
verbose=FALSE): update, if necessary, an object of class
AffyBatch to its current class definition. verbose=TRUE
provides details about the conversion process.
Note
This class is better described in the vignette.
See Also
related methods merge.AffyBatch,
pairs.AffyBatch, and
eSet
Examples
if (require(affydata)) {
## load example
data(Dilution)
## nice print
print(Dilution)
pm(Dilution)[1:5,]
mm(Dilution)[1:5,]
## get indexes for the PM probes for the affyID "1900_at"
mypmindex <- pmindex(Dilution,"1900_at")
## same operation using the primitive
mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
## get the probe intensities from the index
intensity(Dilution)[mypmindex, ]
description(Dilution) ##we can also use the methods of eSet
sampleNames(Dilution)
abstract(Dilution)
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'license()' or 'licence()' for distribution details.
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/AffyBatch-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AffyBatch-class
> ### Title: Class AffyBatch
> ### Aliases: AffyBatch-class AffyBatch,ANY AffyBatch probes geneNames
> ### geneNames<- getCdfInfo image indexProbes intensity<- intensity
> ### pmindex mmindex probeset $.AffyBatch cdfName cdfName,AffyBatch-method
> ### checkValidFilenames probes,AffyBatch-method exprs,AffyBatch-method
> ### exprs<-,AffyBatch,ANY-method se.exprs,AffyBatch-method
> ### se.exprs<-,AffyBatch-method featureNames,AffyBatch-method
> ### featureNames<-,AffyBatch-method geneNames,AffyBatch-method
> ### geneNames<-,AffyBatch,ANY-method getCdfInfo,AffyBatch-method
> ### image,AffyBatch-method initialize,AffyBatch-method
> ### indexProbes,AffyBatch-method intensity<-,AffyBatch-method
> ### intensity,AffyBatch-method pmindex,AffyBatch-method
> ### mmindex,AffyBatch-method probeset,AffyBatch-method
> ### boxplot,AffyBatch-method dim,AffyBatch-method row,AffyBatch-method
> ### col,AffyBatch-method show,AffyBatch-method pm,AffyBatch-method
> ### pm<-,AffyBatch,ANY-method mm,AffyBatch-method
> ### mm<-,AffyBatch,ANY-method probeNames,AffyBatch-method
> ### hist,AffyBatch-method [<-,AffyBatch-method [,AffyBatch-method
> ### [[,AffyBatch-method length,AffyBatch-method
> ### bg.correct,AffyBatch,character-method
> ### indexProbes,AffyBatch,character-method
> ### indexProbes,AffyBatch,missing-method
> ### computeExprSet,AffyBatch,character,character-method
> ### cdfName,AffyBatch-method updateObject,AffyBatch-method
> ### Keywords: classes
>
> ### ** Examples
>
> if (require(affydata)) {
+ ## load example
+ data(Dilution)
+
+ ## nice print
+ print(Dilution)
+
+ pm(Dilution)[1:5,]
+ mm(Dilution)[1:5,]
+
+ ## get indexes for the PM probes for the affyID "1900_at"
+ mypmindex <- pmindex(Dilution,"1900_at")
+ ## same operation using the primitive
+ mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
+ ## get the probe intensities from the index
+ intensity(Dilution)[mypmindex, ]
+
+ description(Dilution) ##we can also use the methods of eSet
+ sampleNames(Dilution)
+ abstract(Dilution)
+ }
Loading required package: affydata
Package LibPath Item
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
Title
[1,] "AffyBatch instance Dilution"
AffyBatch object
size of arrays=640x640 features (35221 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes=
[1] "Gene Logic is making available two studies of Affymetrix GeneChip expression data. The first study consists of a dilution/mixture study with five replicates per condition, with dilution series of two separate RNA sources and mixtures of RNA from these two sources. These were run on HG-u95A version 2 chips, and there are 75 chips in this set. The dilution study data set is available as of Feb 14th,2002.\n"
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf'
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf'
>
>
>
>
>
> dev.off()
null device
1
>