flowCore: Basic structures for flow cytometry data


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Documentation for package `flowCore' version 1.0.2

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A B C D E F G I K L M N P Q R S T misc

!,filter-method Filter FCS files
$,flowSet,character-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
$.flowFrame 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
%&% Take the intersection of two filters with subset semantics
%&%,ANY-method Take the intersection of two filters with subset semantics
%&%-methods Take the intersection of two filters with subset semantics
%in% Methods for Function %in% in Package `flowCore'
%in%,ANY,filterResult-method Methods for Function %in% in Package `flowCore'
%in%,ANY,multipleFilterResult-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,complementFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,ellipsoidGate-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,filterResult-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,intersectFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,kmeansFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,norm2Filter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,polygonGate-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,rectangleGate-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,sampleFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,subsetFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,transformFilter-method Methods for Function %in% in Package `flowCore'
%in%,flowFrame,unionFilter-method Methods for Function %in% in Package `flowCore'
%in%-methods Methods for Function %in% in Package `flowCore'
%on% Methods for Function %on% in Package `flowCore'
%on%,filter,transformList-method Methods for Function %on% in Package `flowCore'
%on%,transformList,flowFrame-method Methods for Function %on% in Package `flowCore'
%on%,transformList,flowSet-method Methods for Function %on% in Package `flowCore'
%on%-methods Methods for Function %on% in Package `flowCore'
%subset% Take the intersection of two filters with subset semantics
%subset%,ANY-method Take the intersection of two filters with subset semantics
%subset%,filter,filter-method Filter FCS files
&,filter,filter-method Filter FCS files
==,filterResult,flowFrame-method Class "filterResult"
==,flowFrame,filterResult-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- A --

arcsinhTransform Create the definition of an arcsinh transformation function (base specified by user) to be applied on a data set

-- B --

biexponentialTransform Compute a transform using the 'biexponential' function
booleanGate,filter-class A class for representing filtering operations to be applied to flow data.

-- C --

coerce Force an Object to Belong to a Class
coerce,complementFilter,logical-method Force an Object to Belong to a Class
coerce,environment,flowSet-method Force an Object to Belong to a Class
coerce,factor,filterResult-method Force an Object to Belong to a Class
coerce,filter,logical-method Force an Object to Belong to a Class
coerce,filterResult,logical-method Force an Object to Belong to a Class
coerce,intersectFilter,logical-method Force an Object to Belong to a Class
coerce,list,flowSet-method Force an Object to Belong to a Class
coerce,logical,filterResult-method Force an Object to Belong to a Class
coerce,logicalFilterResult,logical-method Force an Object to Belong to a Class
coerce,numeric,filterResult-method Force an Object to Belong to a Class
coerce,randomFilterResult,logical-method Force an Object to Belong to a Class
coerce,subsetFilter,logical-method Force an Object to Belong to a Class
coerce,unionFilter,logical-method Force an Object to Belong to a Class
colnames,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
colnames,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
colnames,transformList-method Class "transformList"
colnames<-,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
colnames<-,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
compensate Compensate for spillover between channels in a flowSet or a flowFrame
compensate,flowFrame,matrix-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
compensate,flowFrame-method Compensate for spillover between channels in a flowSet or a flowFrame
compensate,flowSet,matrix-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
compensate,flowSet-method Compensate for spillover between channels in a flowSet or a flowFrame
compensate,matrix-method Compensate for spillover between channels in a flowSet or a flowFrame

-- D --

decisionTreeGate,filter-class A class for representing filtering operations to be applied to flow data.
description,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description<-,flowFrame,character-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
draw,filter,flowFrame-method Filter FCS files

-- E --

each_col Function to apply methods over flowFrame margins
each_col,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
each_row Function to apply methods over flowFrame margins
each_row,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
ellipsoidGate Define ellipsoidal filter boundaries
ellipsoidGate,filter-class A class for representing filtering operations to be applied to flow data.
ellipsoidGate-class Define ellipsoidal filter boundaries
exprs,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
exprs<-,flowFrame,matrix-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- F --

featureNames,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
filter Filter FCS files
filter,filter-method A class for representing filtering operations to be applied to flow data.
filter,flowFrame 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
filter,flowFrame,filter-method Filter FCS files
filter,flowFrame,norm2Filter Filter FCS files
filter,flowFrame,polygonGate Filter FCS files
filter,flowFrame,rectangleGate Filter FCS files
filter,flowSet,filter-method Filter FCS files
filter,flowSet,list-method Filter FCS files
filter-class A class for representing filtering operations to be applied to flow data.
filterDetails Obtain details about a filter operation
filterDetails,filterResult,ANY-method Obtain details about a filter operation
filterDetails,filterResult,missing-method Obtain details about a filter operation
filterDetails-methods Obtain details about a filter operation
filterDetails<-,filterResult,character,ANY-method Obtain details about a filter operation
filterDetails<-,filterResult,character,filter-method Obtain details about a filter operation
filterDetails<-,filterResult,character,setOperationFilter-method Obtain details about a filter operation
filtergate,filter-class A class for representing filtering operations to be applied to flow data.
filterResult-class Class "filterResult"
flowFrame 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
flowFrame-class 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
flowSet 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
flowSet-class 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
fsApply Apply a Function over values in a flowSet
fsApply,flowSet,ANY Apply a Function over values in a flowSet
fsApply,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays

-- G --

GvHD Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)

-- I --

identifier Retrieve the GUID of a Object
identifier,filter-method Retrieve the GUID of a Object
identifier,filterResult-method Retrieve the GUID of a Object
identifier,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
identifier-methods Retrieve the GUID of a Object

-- K --

keyword Methods to retrieve keywords of a flowFrame
keyword,flowFrame,character-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
keyword,flowFrame,function-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
keyword,flowFrame,list-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
keyword,flowFrame,missing-method Methods to retrieve keywords of a flowFrame
keyword,flowSet,list-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
keyword-methods Methods to retrieve keywords of a flowFrame
kmeansFilter One dimensional k-means filters
kmeansFilter-class One dimensional k-means filters

-- L --

length,filter-method Filter FCS files
length,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
length,kmeansFilter-method One dimensional k-means filters
length,multipleFilterResult-method Class "multipleFilterResult"
linearTransform Create the definition of a linear transformation function to be applied on a data set
lnTransform Create the definition of a ln transformation function (natural logarthim) to be applied on a data set
logicalFilterResult-class Class "logicalFilterResult"
logicleTransform Compute a transform using the 'logicle' function
logTransform Create the definition of a log transformation function (base specified by user) to be applied on a data set

-- M --

multiFilter-class Class to represent list of filter
multipleFilterResult-class Class "multipleFilterResult"

-- N --

names,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
names,multipleFilterResult-method Class "multipleFilterResult"
ncol,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
norm2Filter Class "norm2Filter"
norm2Filter,filter-class A class for representing filtering operations to be applied to flow data.
norm2Filter-class Class "norm2Filter"
nrow,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- P --

parameters Methods to retrieve FCS parameters from a flowFrame
parameters,filter-method Methods to retrieve FCS parameters from a flowFrame
parameters,flowFrame,missing-method Methods to retrieve FCS parameters from a flowFrame
parameters,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
pData,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
phenoData,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
phenoData<-,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
phenoData<-,flowSet,phenoData-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
plot,flowFrame,character-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
plot,flowFrame,filter-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
plot,flowFrame,missing-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
polygonGate Define filter boundaries
polygonGate,filter-class A class for representing filtering operations to be applied to flow data.
polygonGate-class Define filter boundaries
polytopeGate Define filter boundaries
polytopeGate-class Define filter boundaries
print.filterSummary Summarize the results after applying a filter

-- Q --

quadraticTransform Create the definition of a quadratic transformation function to be applied on a data set

-- R --

randomFilterResult-class Class "randomFilterResult"
rbind2,flowSet,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
rbind2,flowSet,missing 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
read.FCS Read an FCS file
read.flowSet Read a set of FCS files
rectangleGate Define filter boundaries
rectangleGate,filter-class A class for representing filtering operations to be applied to flow data.
rectangleGate-class Define filter boundaries

-- S --

sampleFilter-class Class "sampleFilter"
sampleNames,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
scaleTransform Create the definition of a scale transformation function to be applied on a data set
setOperationFilter-class Class "setOperationFilter"
show,filter-method Filter FCS files
show,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
show,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
show,kmeansFilter-method One dimensional k-means filters
show,polygonGate-method Define filter boundaries
show,rectangleGate-method Define filter boundaries
show,sampleFilter-method Class "sampleFilter"
spillover Compute a spillover matrix from a flowSet
spillover,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
spillover,flowSet-method Compute a spillover matrix from a flowSet
split,flowFrame,filter-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
split,flowFrame,logicalFilterResult-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
split,flowFrame,multipleFilterResult-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
split,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
split,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
Subset Subset a flowFrame or a flowSet
Subset,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
Subset,flowFrame,filter-metho 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
Subset,flowFrame,filter-method Subset a flowFrame or a flowSet
Subset,flowFrame,logical-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
Subset,flowSet,ANY 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
Subset,flowSet,ANY-method Subset a flowFrame or a flowSet
Subset,flowSet,list-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
summary Summarize the results after applying a filter
summary,filter-method Filter FCS files
summary,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
summary,multipleFilterResult-method Class "multipleFilterResult"
summary,rectangleGate-method Define filter boundaries
summary,subsetFilter-method Summarize the results after applying a filter
summary,transform-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
summary-methods Summarize the results after applying a filter

-- T --

transform 'transform': a class for transforming flow-cytometry data by applying scale factors.
transform,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
transform,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
transform,missing-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
transform-class 'transform': a class for transforming flow-cytometry data by applying scale factors.
transformFilter-class A class for encapsulating a filter to be performed on transformed parameters
transformList-class Class "transformList"
transformMap-class A class for mapping transforms between parameters
truncateTransform Create the definition of a trucate tranformation function to be applied on a data set

-- misc --

[,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
[,flowFrame,filter-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
[,flowFrame,filterResult-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
[,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[[,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[[,multipleFilterResult-method Class "multipleFilterResult"
[[<-,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
|,filter,filter-method Filter FCS files