flowCore: Basic structures for flow cytometry data


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Documentation for package ‘flowCore’ version 1.10.0

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-- --

!,filter-method A class for representing filtering operations to be applied to flow data.
$,filterSummary,ANY-method Class "filterSummary"
$,flowSet,character-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
$,workFlow,character-method Class "workFlow"
$.flowFrame 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
%&% Take the intersection of two filters
%&%,ANY-method Take the intersection of two filters
%&%,filter,filter-method Take the intersection of two filters
%&%-methods Take the intersection of two filters
%in% Filter-specific membership methods
%in%,ANY,filterReference-method Filter-specific membership methods
%in%,ANY,filterResult-method Filter-specific membership methods
%in%,ANY,manyFilterResult-method Filter-specific membership methods
%in%,ANY,multipleFilterResult-method Filter-specific membership methods
%in%,flowFrame,boundaryFilter-method Filter-specific membership methods
%in%,flowFrame,complementFilter-method Filter-specific membership methods
%in%,flowFrame,curv1Filter-method Filter-specific membership methods
%in%,flowFrame,curv2Filter-method Filter-specific membership methods
%in%,flowFrame,ellipsoidGate-method Filter-specific membership methods
%in%,flowFrame,expressionFilter-method Filter-specific membership methods
%in%,flowFrame,filterResult-method Filter-specific membership methods
%in%,flowFrame,intersectFilter-method Filter-specific membership methods
%in%,flowFrame,kmeansFilter-method Filter-specific membership methods
%in%,flowFrame,norm2Filter-method Filter-specific membership methods
%in%,flowFrame,polygonGate-method Filter-specific membership methods
%in%,flowFrame,polytopeGate-method Filter-specific membership methods
%in%,flowFrame,quadGate-method Filter-specific membership methods
%in%,flowFrame,rectangleGate-method Filter-specific membership methods
%in%,flowFrame,sampleFilter-method Filter-specific membership methods
%in%,flowFrame,subsetFilter-method Filter-specific membership methods
%in%,flowFrame,timeFilter-method Filter-specific membership methods
%in%,flowFrame,transformFilter-method Filter-specific membership methods
%in%,flowFrame,unionFilter-method Filter-specific membership methods
%in%-methods Filter-specific membership methods
%on% Methods for Function \%on\% in Package 'flowCore'
%on%,ANY,flowSet-method Methods for Function \%on\% in Package 'flowCore'
%on%,filter,parameterTransform-method Methods for Function \%on\% in Package 'flowCore'
%on%,filter,transform-method Methods for Function \%on\% in Package 'flowCore'
%on%,filter,transformList-method Methods for Function \%on\% in Package 'flowCore'
%on%,parameterTransform,flowFrame-method Methods for Function \%on\% in Package 'flowCore'
%on%,transform,flowFrame-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
%subset%,ANY-method Take the intersection of two filters
%subset%,filter,filter-method Take the intersection of two filters
%subset%,filterSet,filter-method Class filterSet
%subset%,list,filter-method Take the intersection of two filters
&,filter,filter-method Take the intersection of two filters
&,filter,list-method Take the intersection of two filters
&,list,filter-method Take the intersection of two filters
*,rectangleGate,rectangleGate-method Class "rectangleGate"
<,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
<=,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
==,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
==,flowFrame,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
>,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
>=,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- A --

action Class "view"
action,view-method Class "view"
actionItem-class Class "actionItem"
actions Class "workFlow"
actions,workFlow-method Class "workFlow"
add Class "workFlow"
add,workFlow,character-method Class "subsetting"
add,workFlow,compensation-method Class "workFlow"
add,workFlow,concreteFilter-method Class "workFlow"
add,workFlow,filterList-method Class "workFlow"
add,workFlow,logical-method Class "subsetting"
add,workFlow,normalization-method Class "normalization"
add,workFlow,numeric-method Class "subsetting"
add,workFlow,subsetting-method Class "subsetting"
add,workFlow,transformList-method Class "workFlow"
alias Class "view"
alias,actionItem-method Class "actionItem"
alias,environment-method Class "workFlow"
alias,view-method Class "view"
alias,workFlow-method Class "workFlow"
arcsinhTransform Create the definition of an arcsinh transformation function (base specified by user) to be applied on a data set
as.data.frame.manyFilterResult Class "manyFilterResult"
asinht Class "asinht"
asinht-class Class "asinht"
assign Class "fcReference" and its subclasses
assign,ANY,ANY,missing,workFlow,missing,missing-method Class "workFlow"
assign,character,ANY,workFlow,missing,missing,missing-method Class "workFlow"
assign,fcReference,ANY,workFlow,missing,missing,missing-method Class "workFlow"
assign,missing,ANY,missing,workFlow,missing,missing-method Class "workFlow"
assign,missing,ANY,workFlow,missing,missing,missing-method Class "workFlow"

-- B --

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

-- C --

c,transformList-method Class "transformList"
call,filter-method Filter FCS files
cbind2,flowFrame,matrix-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
cbind2,flowFrame,numeric-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
char2ExpressionFilter Class "expressionFilter"
character,filter-method Filter FCS files
characterOrTransformation-class Class "characterOrTransformation"
cleanup Read an FCS file
coerce Convert an object to another class
coerce,call,filter-method Convert an object to another class
coerce,character,filter-method Convert an object to another class
coerce,complementFilter,call-method Convert an object to another class
coerce,complementFilter,logical-method Convert an object to another class
coerce,ellipsoidGate,polygonGate-method Convert an object to another class
coerce,environment,flowSet-method Convert an object to another class
coerce,factor,filterResult-method Convert an object to another class
coerce,filter,call-method Convert an object to another class
coerce,filter,logical-method Convert an object to another class
coerce,filterReference,call-method Convert an object to another class
coerce,filterReference,concreteFilter-method Convert an object to another class
coerce,filterResult,logical-method Convert an object to another class
coerce,filterResultList,list-method Convert an object to another class
coerce,filterSet,list-method Convert an object to another class
coerce,filterSummary,data.frame-method Class "filterSummary"
coerce,flowFrame,filterSet-method Convert an object to another class
coerce,flowFrame,flowSet-method Convert an object to another class
coerce,flowSet,flowFrame-method Convert an object to another class
coerce,flowSet,list-method Convert an object to another class
coerce,formula,filter-method Convert an object to another class
coerce,gateView,filterResult-method Convert an object to another class
coerce,intersectFiler,call-method Convert an object to another class
coerce,intersectFilter,call-method Take the intersection of two filters
coerce,intersectFilter,logical-method Convert an object to another class
coerce,list,filterResultList-method Convert an object to another class
coerce,list,filterSet-method Convert an object to another class
coerce,list,flowSet-method Convert an object to another class
coerce,list,transformList-method Convert an object to another class
coerce,logical,filterResult-method Convert an object to another class
coerce,logicalFilterResult,logical-method Convert an object to another class
coerce,name,filter-method Convert an object to another class
coerce,nullParameter,character-method Convert an object to another class
coerce,numeric,filterResult-method Convert an object to another class
coerce,parameters,character-method Convert an object to another class
coerce,randomFilterResult,logical-method Convert an object to another class
coerce,ratio,character-method Convert an object to another class
coerce,rectangleGate,polygonGate-method Convert an object to another class
coerce,subsetFilter,call-method Convert an object to another class
coerce,subsetFilter,logical-method Convert an object to another class
coerce,transform,character-method Convert an object to another class
coerce,unionFilter,call-method Convert an object to another class
coerce,unionFilter,logical-method Convert an object to another class
coerce,unitytransform,character-method Convert an object to another class
colnames 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
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': a class for storing observed quantitative properties for a population of cells from a FACS run
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 Class "compensation"
compensate,flowFrame,compensation-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
compensate,flowFrame,data.frame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
compensate,flowFrame,matrix-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
compensate,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
compensate,flowSet,matrix-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
compensateActionItem Class "compensateActionItem"
compensateActionItem-class Class "compensateActionItem"
compensatedParameter Class "compensatedParameter"
compensatedParameter-class Class "compensatedParameter"
compensateView Class "compensateView"
compensateView-class Class "compensateView"
compensation Class "compensation"
compensation-class Class "compensation"
complementFilter-class Class "setOperationFilter"
concreteFilter-class Class "concreteFilter"
curv1Filter Class "curv1Filter"
curv1Filter-class Class "curv1Filter"
curv2Filter Class "curv2Filter"
curv2Filter-class Class "curv2Filter"

-- D --

Data Class "view"
Data,view-method Class "view"
decisionTreeGate,filter-class A class for representing filtering operations to be applied to flow data.
description 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description<-,flowFrame,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description<-,flowFrame,list-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
dg1polynomial Class "dg1polynomial"
dg1polynomial-class Class "dg1polynomial"
dim 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
dim,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- E --

each_col Method to apply functions over flowFrame margins
each_col,flowFrame-method Method to apply functions over flowFrame margins
each_col-methods Method to apply functions over flowFrame margins
each_row Method to apply functions over flowFrame margins
each_row,flowFrame-method Method to apply functions over flowFrame margins
each_row-methods Method to apply functions over flowFrame margins
EHtrans Class "EHtrans"
EHtrans-class Class "EHtrans"
ellipsoidGate Class "ellipsoidGate"
ellipsoidGate,filter-class A class for representing filtering operations to be applied to flow data.
ellipsoidGate-class Class "ellipsoidGate"
eval,asinht,missing,missing-method Class "asinht"
eval,compensatedParameter,missing,missing-method Class "compensatedParameter"
eval,dg1polynomial,missing,missing-method Class "dg1polynomial"
eval,EHtrans,missing,missing-method Class "EHtrans"
eval,exponential,missing,missing-method Class "exponential"
eval,filterReference,missing,missing-method Class filterReference
eval,hyperlog,missing,missing-method Class "hyperlog"
eval,invsplitscale,missing,missing-method Class "invsplitscale"
eval,logarithm,missing,missing-method Class "logarithm"
eval,quadratic,missing,missing-method Class "quadratic"
eval,ratio,missing,missing-method Class "ratio"
eval,sinht,missing,missing-method Class "sinht"
eval,splitscale,missing,missing-method Class "splitscale"
eval,squareroot,missing,missing-method Class "squareroot"
eval,transformReference,missing,missing-method Class "transformReference"
eval,unitytransform,missing,missing-method Class "unitytransform"
exponential Class "exponential"
exponential-class Class "exponential"
expressionFilter Class "expressionFilter"
expressionFilter-class Class "expressionFilter"
exprs 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
exprs,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
exprs<- 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
exprs<-,flowFrame,ANY-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 --

fcActionReference Class "fcReference" and its subclasses
fcActionReference-class Class "fcReference" and its subclasses
fcAliasReference Class "fcReference" and its subclasses
fcAliasReference-class Class "fcReference" and its subclasses
fcCompensateReference Class "fcReference" and its subclasses
fcCompensateReference-class Class "fcReference" and its subclasses
fcDataReference Class "fcReference" and its subclasses
fcDataReference-class Class "fcReference" and its subclasses
fcFilterReference Class "fcReference" and its subclasses
fcFilterReference-class Class "fcReference" and its subclasses
fcFilterResultReference Class "fcReference" and its subclasses
fcFilterResultReference-class Class "fcReference" and its subclasses
fcNormalizationReference Class "fcReference" and its subclasses
fcNormalizationReference-class Class "fcReference" and its subclasses
fcNullReference Class "fcReference" and its subclasses
fcNullReference-class Class "fcReference" and its subclasses
fcReference Class "fcReference" and its subclasses
fcReference-class Class "fcReference" and its subclasses
fcStructureReference-class Class "fcReference" and its subclasses
fcSubsettingReference Class "fcReference" and its subclasses
fcSubsettingReference-class Class "fcReference" and its subclasses
fcTransformReference Class "fcReference" and its subclasses
fcTransformReference-class Class "fcReference" and its subclasses
fcTreeReference Class "fcReference" and its subclasses
fcTreeReference-class Class "fcReference" and its subclasses
fcViewReference Class "fcReference" and its subclasses
fcViewReference-class Class "fcReference" and its subclasses
featureNames 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
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,filter-method Filter FCS files
filter,flowFrame,filterSet-method Filter FCS files
filter,flowFrame,norm2Filter Filter FCS files
filter,flowFrame,polygonGate Filter FCS files
filter,flowFrame,rectangleGate Filter FCS files
filter,flowFrame-method Filter FCS files
filter,flowSet,filter-method Filter FCS files
filter,flowSet,filterList-method Filter FCS files
filter,flowSet,filterSet-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.
filter-on-methods Methods for Function \%on\% in Package 'flowCore'
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<- 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.
filterList Class "filterList"
filterList-class Class "filterList"
filterReference Class filterReference
filterReference,environment,character-method Class filterReference
filterReference,filterSet,character-method Class filterSet
filterReference-class Class filterReference
filterResult Class "filterResult"
filterResult-class Class "filterResult"
filterResultList Class "filterResultList"
filterResultList-class Class "filterResultList"
filterSet Class filterSet
filterSet-class Class filterSet
filterSummary Class "filterSummary"
filterSummary-class Class "filterSummary"
filterSummaryList Class "filterSummaryList"
filterSummaryList-class Class "filterSummaryList"
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
formula,filter-method Filter FCS files
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 --

gate Class "gateActionItem"
gate,gateActionItem-method Class "gateActionItem"
gateActionItem Class "gateActionItem"
gateActionItem-class Class "gateActionItem"
gateView Class "gateView"
gateView-class Class "gateView"
get Class "fcReference" and its subclasses
get,character,missing,workFlow,missing,missing-method Class "workFlow"
get,character,workFlow,missing,missing,missing-method Class "workFlow"
get,fcNullReference,missing,missing,missing,missing-method Class "fcReference" and its subclasses
get,fcReference,missing,missing,missing,missing-method Class "fcReference" and its subclasses
GvHD Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)

-- H --

head,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
hyperlog Class "hyperlog"
hyperlog-class Class "hyperlog"

-- I --

identifier Retrieve the GUID of flowCore objects
identifier,actionItem-method Class "actionItem"
identifier,compensation-method Class "compensation"
identifier,fcReference-method Class "fcReference" and its subclasses
identifier,filter-method Retrieve the GUID of flowCore objects
identifier,filterList-method Class "filterList"
identifier,filterReference-method Retrieve the GUID of flowCore objects
identifier,filterResult-method Retrieve the GUID of flowCore objects
identifier,filterSet,character-method Class filterSet
identifier,filterSet-method Class filterSet
identifier,flowFrame-method Retrieve the GUID of flowCore objects
identifier,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
identifier,normalization-method Class "normalization"
identifier,NULL-method Class "view"
identifier,subsetting-method Class "subsetting"
identifier,transform-method Retrieve the GUID of flowCore objects
identifier,transformList-method Class "transformList"
identifier,view-method Class "view"
identifier-methods Retrieve the GUID of flowCore objects
identifier<- Retrieve the GUID of flowCore objects
identifier<-,compensation,character-method Class "compensation"
identifier<-,filter,character-method Filter FCS files
identifier<-,filterList,character-method Class "filterList"
identifier<-,flowFrame,ANY-method Retrieve the GUID of flowCore objects
identifier<-,flowFrame-method Retrieve the GUID of flowCore objects
identifier<-,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
identifier<-,normalization,character-method Class "normalization"
identifier<-,subsetting,character-method Class "subsetting"
identifier<-,transformList,character-method Class "transformList"
initialize,dg1polynomial-method Class "dg1polynomial"
initialize,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
initialize,parameterFilter-method Class "parameterFilter"
initialize,ratio-method Class "ratio"
initialize,singleParameterTransform-method Class "singleParameterTransform"
intersectFilter-class Class "setOperationFilter"
intersectFilter-method Take the intersection of two filters
invsplitscale Class "invsplitscale"
invsplitscale-class Class "invsplitscale"
isFCSfile Read an FCS file
isNull Class "fcReference" and its subclasses
isNull,fcReference-method Class "fcReference" and its subclasses

-- J --

journal Class "workFlow"
journal,environment-method Class "workFlow"
journal,workFlow-method Class "workFlow"

-- K --

keyword Methods to retrieve keywords of a flowFrame
keyword,flowFrame,character-method Methods to retrieve keywords of a flowFrame
keyword,flowFrame,function-method Methods to retrieve keywords of a flowFrame
keyword,flowFrame,list-method Methods to retrieve keywords of a flowFrame
keyword,flowFrame,missing-method Methods to retrieve keywords of a flowFrame
keyword,flowSet,ANY-method Methods to retrieve keywords of a flowFrame
keyword,flowSet,list-method Methods to retrieve keywords of a flowFrame
keyword-methods Methods to retrieve keywords of a flowFrame
keyword<- Methods to retrieve keywords of a flowFrame
keyword<-,flowFrame,ANY-method Methods to retrieve keywords of a flowFrame
keyword<-,flowFrame,character-method Methods to retrieve keywords of a flowFrame
keyword<-,flowFrame,list-method Methods to retrieve keywords of a flowFrame
keyword<-,flowSet,list-method Methods to retrieve keywords of a flowFrame
kmeansFilter Class "kmeansFilter"
kmeansFilter-class Class "kmeansFilter"

-- L --

length,filter-method Filter FCS files
length,filterReference-method Class filterReference
length,filterSummary-method Class "filterSummary"
length,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
length,kmeansFilter-method Class "kmeansFilter"
length,logicalFilterResult-method Class "logicalFilterResult"
length,manyFilterResult-method Class "manyFilterResult"
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
logarithm Class "logarithm"
logarithm-class Class "logarithm"
logicalFilterResult Class "logicalFilterResult"
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
ls Class "workFlow"
ls,workFlow,missing,missing,missing,character-method Class "workFlow"
ls,workFlow,missing,missing,missing,missing-method Class "workFlow"

-- M --

manyFilterResult Class "manyFilterResult"
manyFilterResult-class Class "manyFilterResult"
mget Class "workFlow"
mget,character,workFlow,missing,missing,missing-method Class "workFlow"
multipleFilterResult Class "multipleFilterResult"
multipleFilterResult-class Class "multipleFilterResult"

-- N --

name,filter-method Filter FCS files
names 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
names,actionItem-method Class "actionItem"
names,filterResultList-method Class "filterResultList"
names,filterSet-method Class filterSet
names,filterSummary-method Class "filterSummary"
names,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
names,logicalFilterResult-method Class "logicalFilterResult"
names,manyFilterResult-method Class "manyFilterResult"
names,multipleFilterResult-method Class "multipleFilterResult"
names,view-method Class "view"
names,workFlow-method Class "workFlow"
names<-,multipleFilterResult,ANY-method Class "multipleFilterResult"
names<-,multipleFilterResult-method Class "multipleFilterResult"
ncol 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
ncol,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
nodes,workFlow-method Class "workFlow"
norm2Filter Class "norm2Filter"
norm2Filter,filter-class A class for representing filtering operations to be applied to flow data.
norm2Filter-class Class "norm2Filter"
normalization Class "normalization"
normalization-class Class "normalization"
normalize Class "normalization"
normalize,flowSet,normalization-method Class "normalization"
normalizeActionItem Class "normalizeActionItem"
normalizeActionItem-class Class "normalizeActionItem"
normalizeView Class "normalizeView"
normalizeView-class Class "normalizeView"
nrow 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
nrow,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

-- P --

parameterFilter-class Class "parameterFilter"
parameters Obtain information about parameters for flow cytometry objects.
parameters,compensation-method Class "compensation"
parameters,filter-method Obtain information about parameters for flow cytometry objects.
parameters,filterReference-method Obtain information about parameters for flow cytometry objects.
parameters,filterResult-method Obtain information about parameters for flow cytometry objects.
parameters,filterResultList-method Class "filterResultList"
parameters,flowFrame,missing-method Obtain information about parameters for flow cytometry objects.
parameters,flowFrame-method Obtain information about parameters for flow cytometry objects.
parameters,manyFilterResult-method Class "manyFilterResult"
parameters,normalization-method Class "normalization"
parameters,nullParameter-method Obtain information about parameters for flow cytometry objects.
parameters,parameterFilter-method Obtain information about parameters for flow cytometry objects.
parameters,parameterTransform-method Obtain information about parameters for flow cytometry objects.
parameters,ratio-method Obtain information about parameters for flow cytometry objects.
parameters,setOperationFilter-method Obtain information about parameters for flow cytometry objects.
parameters,transform-method Obtain information about parameters for flow cytometry objects.
parameters,transformReference-method Class "transformReference"
parameters-class Class "parameters"
parameters<- Obtain information about parameters for flow cytometry objects.
parameters<-,dg1polynomial,character-method Class "dg1polynomial"
parameters<-,dg1polynomial,parameters-method Class "dg1polynomial"
parameters<-,dg1polynomial,transform-method Obtain information about parameters for flow cytometry objects.
parameters<-,flowFrame,AnnotatedDataFrame-method Obtain information about parameters for flow cytometry objects.
parameters<-,parameterFilter,character-method Obtain information about parameters for flow cytometry objects.
parameters<-,parameterFilter,list-method Obtain information about parameters for flow cytometry objects.
parameters<-,parameterFilter,transform-method Obtain information about parameters for flow cytometry objects.
parameters<-,singleParameterTransform,character-method Obtain information about parameters for flow cytometry objects.
parameters<-,singleParameterTransform,transform-method Obtain information about parameters for flow cytometry objects.
parameterTransform-class Class "parameterTransform"
parent Class "view"
parent,actionItem-method Class "actionItem"
parent,NULL-method Class "view"
parent,view-method Class "view"
pData,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
pData<-,flowSet,data.frame-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,ANY-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
plot,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
plot,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
plot,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
plot,workFlow,missing-method Class "workFlow"
polygonGate Class "polygonGate"
polygonGate,filter-class A class for representing filtering operations to be applied to flow data.
polygonGate-class Class "polygonGate"
polytopeGate Define filter boundaries
polytopeGate-class Define filter boundaries
print,compensateActionItem-method Class "compensateActionItem"
print,filterSummary-method Class "filterSummary"
print,gateActionItem-method Class "gateActionItem"
print,normalizeActionItem-method Class "normalizeActionItem"
print,subsettingActionItem-method Class "subsettingActionItem"
print,transformActionItem-method Class "transformActionItem"
print,view-method Class "view"

-- Q --

quadGate Class "quadGate"
quadGate-class Class "quadGate"
quadratic Class "quadratic"
quadratic-class Class "quadratic"
quadraticTransform Create the definition of a quadratic transformation function to be applied on a data set

-- R --

randomFilterResult-class Class "randomFilterResult"
range 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
range,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
ratio Class "ratio"
ratio-class Class "ratio"
rbind2,flowFrame,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
rbind2,flowSet,flowFrame-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
rbind2,flowSet,flowSet,missing-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
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
rbind2,flowSet,missing-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
read.FCS Read an FCS file
read.FCSheader Read the TEXT section of a FCS file
read.flowSet Read a set of FCS files
rectangleGate Class "rectangleGate"
rectangleGate,filter-class A class for representing filtering operations to be applied to flow data.
rectangleGate-class Class "rectangleGate"
Rm Class "fcReference" and its subclasses
Rm,actionItem,workFlow,character-method Class "actionItem"
Rm,character,workFlow,character-method Class "workFlow"
Rm,compensateActionItem,workFlow,character-method Class "compensateActionItem"
Rm,compensateView,workFlow,character-method Class "compensateView"
Rm,fcNullReference,missing,character-method Class "fcReference" and its subclasses
Rm,fcReference,missing,character-method Class "fcReference" and its subclasses
Rm,fcReference,workFlow,character-method Class "fcReference" and its subclasses
Rm,gateActionItem,workFlow,character-method Class "gateActionItem"
Rm,gateView,workFlow,character-method Class "gateView"
Rm,normalizeActionItem,workFlow,character-method Class "normalizeActionItem"
Rm,normalizeView,workFlow,character-method Class "normalizeView"
Rm,subsettingActionItem,workFlow,character-method Class "subsettingActionItem"
Rm,subsettingView,workFlow,character-method Class "subsettingView"
Rm,transformActionItem,workFlow,character-method Class "transformActionItem"
Rm,transformView,workFlow,character-method Class "transformView"
Rm,view,workFlow,character-method Class "view"

-- S --

sampleFilter Class "sampleFilter"
sampleFilter-class Class "sampleFilter"
sampleNames,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
sampleNames<-,flowSet,ANY-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,boundaryFilter-method Class "boundaryFilter"
show,compensateActionItem-method Class "compensateActionItem"
show,compensation-method Class "compensation"
show,complementFilter-method Class "setOperationFilter"
show,curv1Filter-method Class "curv1Filter"
show,curv2Filter-method Class "curv2Filter"
show,ellipsoidGate-method Class "ellipsoidGate"
show,expressionFilter-method Class "expressionFilter"
show,fcNullReference-method Class "fcReference" and its subclasses
show,fcReference-method Class "fcReference" and its subclasses
show,filter-method Filter FCS files
show,filterList-method Class "filterList"
show,filterReference-method Class filterReference
show,filterResult-method Class "filterResult"
show,filterResultList-method Class "filterResultList"
show,filterSet-method Class filterSet
show,filterSummary-method Class "filterSummary"
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,gateActionItem-method Class "gateActionItem"
show,intersectFilter-method Class "setOperationFilter"
show,kmeansFilter-method Class "kmeansFilter"
show,manyFilterResult-method Class "manyFilterResult"
show,multipleFilterResult-method Class "multipleFilterResult"
show,norm2Filter-method Class "norm2Filter"
show,normalizeActionItem-method Class "normalizeActionItem"
show,polygonGate-method Class "polygonGate"
show,polytopeGate-method Define filter boundaries
show,quadGate-method Class "quadGate"
show,rectangleGate-method Class "rectangleGate"
show,sampleFilter-method Class "sampleFilter"
show,subsetFilter-method Class "setOperationFilter"
show,subsetting-method Class "subsetting"
show,subsettingActionItem-method Class "subsettingActionItem"
show,timeFilter-method Class "timeFilter"
show,transform-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
show,transformActionItem-method Class "transformActionItem"
show,transformFilter-method A class for encapsulating a filter to be performed on transformed parameters
show,transformMap-method A class for mapping transforms between parameters
show,unionFilter-method Class "setOperationFilter"
show,unitytransform-method Class "unitytransform"
show,view-method Class "view"
show,workFlow-method Class "workFlow"
singleParameterTransform-class Class "singleParameterTransform"
sinht Class "sinht"
sinht-class Class "sinht"
sort,filterSet-method Class filterSet
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 Methods to split flowFrames and flowSets according to filters
split,flowFrame,ANY-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,character-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,factor-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,filter-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,filterSet-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,logicalFilterResult-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,manyFilterResult-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,multipleFilterResult-method Methods to split flowFrames and flowSets according to filters
split,flowFrame,numeric-method Methods to split flowFrames and flowSets according to filters
split,flowSet,ANY-method Methods to split flowFrames and flowSets according to filters
split,flowSet,character-method Methods to split flowFrames and flowSets according to filters
split,flowSet,factor-method Methods to split flowFrames and flowSets according to filters
split,flowSet,filter-method Methods to split flowFrames and flowSets according to filters
split,flowSet,filterResult-method Methods to split flowFrames and flowSets according to filters
split,flowSet,filterResultList-method Class "filterResultList"
split,flowSet,list-method Methods to split flowFrames and flowSets according to filters
split,flowSet,numeric-method Methods to split flowFrames and flowSets according to filters
split-methods Methods to split flowFrames and flowSets according to filters
splitscale Class "splitscale"
splitscale-class Class "splitscale"
splitScaleTransform Compute the split-scale transformation describe by FL. Battye
squareroot Class "squareroot"
squareroot-class Class "squareroot"
Subset Subset a flowFrame or a flowSet
Subset,flowFrame,filter-method Subset a flowFrame or a flowSet
Subset,flowFrame,logical-method Subset a flowFrame or a flowSet
Subset,flowFrame-method Subset a flowFrame or a flowSet
Subset,flowSet,ANY Subset a flowFrame or a flowSet
Subset,flowSet,ANY-method Subset a flowFrame or a flowSet
Subset,flowSet,filterResultList-method Subset a flowFrame or a flowSet
Subset,flowSet,list-method Subset a flowFrame or a flowSet
subsetFilter-class Class "setOperationFilter"
subsetFilter-method Take the intersection of two filters
subsetting Class "subsetting"
subsetting-class Class "subsetting"
subsettingActionItem Class "subsettingActionItem"
subsettingActionItem-class Class "subsettingActionItem"
subsettingView Class "subsettingView"
subsettingView-class Class "subsettingView"
summarizeFilter Methods for function summarizeFilter
summarizeFilter,filterResult,filter-method Methods for function summarizeFilter
summarizeFilter,filterResult,filterReference-method Methods for function summarizeFilter
summarizeFilter,filterResult,parameterFilter-method Methods for function summarizeFilter
summarizeFilter,filterResult,subsetFilter-method Methods for function summarizeFilter
summarizeFilter,logicalFilterResult,norm2Filter-method Methods for function summarizeFilter
summarizeFilter,logicalFilterResult,parameterFilter-method Methods for function summarizeFilter
summarizeFilter,multipleFilterResult,curv1Filter-method Methods for function summarizeFilter
summarizeFilter,multipleFilterResult,curv2Filter-method Methods for function summarizeFilter
summarizeFilter,multipleFilterResult,parameterFilter-method Methods for function summarizeFilter
summarizeFilter-methods Methods for function summarizeFilter
summary Class "filterSummary"
summary,filter-method Filter FCS files
summary,filterReference-method Class filterReference
summary,filterResult-method Class "filterResult"
summary,filterResultList-method Class "filterResultList"
summary,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
summary,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
summary,gateActionItem-method Class "gateActionItem"
summary,gateView-method Class "gateView"
summary,logicalFilterResult-method Class "logicalFilterResult"
summary,manyFilterResult-method Class "manyFilterResult"
summary,multipleFilterResult-method Class "multipleFilterResult"
summary,rectangleGate-method Class "rectangleGate"
summary,subsetFilter-method Class "setOperationFilter"
summary,transform-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
summary,workFlow-method Class "workFlow"

-- T --

tail,flowFrame-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
timeFilter Class "timeFilter"
timeFilter-class Class "timeFilter"
timeFilter-class Class "timeFilter"
toTable Class "filterSummary"
toTable,filterSummary-method Class "filterSummary"
toTable,filterSummaryList-method Class "filterSummaryList"
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.
transformActionItem Class "transformActionItem"
transformActionItem-class Class "transformActionItem"
transformation-class Class "transformation"
transformFilter A class for encapsulating a filter to be performed on transformed parameters
transformFilter-class A class for encapsulating a filter to be performed on transformed parameters
transformList Class "transformList"
transformList-class Class "transformList"
transformMap A class for mapping transforms between parameters
transformMap-class A class for mapping transforms between parameters
transformReference Class "transformReference"
transformReference-class Class "transformReference"
transformView Class "transformView"
transformView-class Class "transformView"
tree Class "workFlow"
tree,environment-method Class "workFlow"
tree,workFlow-method Class "workFlow"
truncateTransform Create the definition of a trucate tranformation function to be applied on a data set

-- U --

undo Class "workFlow"
unionFilter-class Class "setOperationFilter"
unitytransform Class "unitytransform"
unitytransform-class Class "unitytransform"

-- V --

varLabels,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varLabels<-,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varLabels<-,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varMetadata,flowSet-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varMetadata<-,flowSet,ANY-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
view Class "view"
view-class Class "view"
views Class "workFlow"
views,workFlow-method Class "workFlow"

-- W --

workFlow Class "workFlow"
workFlow-class Class "workFlow"

-- X --

xyplot,formula,gateView-method Class "gateView"
xyplot,formula,view-method Class "view"
xyplot,view,missing-method Class "view"

-- misc --

[,filterResultList,ANY-method Class "filterResultList"
[,filterSet,character-method Class filterSet
[,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
[,multipleFilterResult,ANY-method Class "multipleFilterResult"
[,rectangleGate,ANY-method Class "rectangleGate"
[,rectangleGate,character-method Class "rectangleGate"
[,workFlow,ANY-method Class "workFlow"
[[,filterResult,ANY-method Class "filterResult"
[[,filterResultList,ANY-method Class "filterResultList"
[[,filterSet,character-method Class filterSet
[[,filterSummary,character-method Class "filterSummary"
[[,filterSummary,numeric-method Class "filterSummary"
[[,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
[[,logicalFilterResult,ANY-method Class "logicalFilterResult"
[[,manyFilterResult,ANY-method Class "manyFilterResult"
[[,manyFilterResult-method Class "manyFilterResult"
[[,multipleFilterResult,ANY-method Class "multipleFilterResult"
[[,multipleFilterResult-method Class "multipleFilterResult"
[[,workFlow,ANY-method Class "workFlow"
[[<-,filterSet,ANY,ANY,filterReference-method Class filterSet
[[<-,filterSet,character,ANY,filter-method Class filterSet
[[<-,filterSet,character,ANY,formula-method Class filterSet
[[<-,filterSet,missing,ANY,filter Class filterSet
[[<-,filterSet,missing,ANY,filter-method Class filterSet
[[<-,filterSet,NULL,ANY,filter-method Class filterSet
[[<-,filterSet,NULL,ANY,formula-method Class filterSet
[[<-,flowFrame-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[[<-,flowSet,ANY,ANY,flowFrame-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
|,filter,filter-method A class for representing filtering operations to be applied to flow data.
|,filter,list-method A class for representing filtering operations to be applied to flow data.
|,list,filter-method A class for representing filtering operations to be applied to flow data.