flowCore: Basic structures for flow cytometry data

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Documentation for package ‘flowCore’ version 1.48.0

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A B C D E F G H I J K L M N P Q R S T U V W X misc

flowCore-package Provides S4 data structures and basic infrastructure and functions to deal with flow cytometry data.

-- A --

action Class "view"
action-method Class "view"
actionItem-class Class "actionItem"
actions Class "workFlow"(deprecated)
actions-method Class "workFlow"(deprecated)
add Class "workFlow"(deprecated)
add-method Class "normalization"
add-method Class "subsetting"
add-method Class "workFlow"(deprecated)
alias Class "view"
alias-method Class "actionItem"
alias-method Class "view"
alias-method Class "workFlow"(deprecated)
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"
asinhtGml2 Class asinhtGml2
asinhtGml2-class Class asinhtGml2
assign Class "fcReference" and its subclasses
assign-method Class "workFlow"(deprecated)

-- 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-method Class "transformList"
call-method Filter FCS files
cbind2-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
char2ExpressionFilter Class "expressionFilter"
character-method Filter FCS files
characterOrTransformation-class Class "characterOrTransformation"
checkOffset Fix the offset when its values recorded in header and TEXT don't agree
cleanup Read an FCS file
coerce Convert an object to another class
coerce-method Convert an object to another class
coerce-method Take the intersection of two filters
coerce-method Class "filterSummary"
colnames-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
colnames-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
colnames-method Class "transformList"
colnames<- 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
colnames<--method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
colnames<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
compensate Class "compensation"
compensate-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
compensate-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"

-- D --

Data Class "view"
Data-method Class "view"
decisionTreeGate,filter-class A class for representing filtering operations to be applied to flow data.
decompensate decompensate a flowFrame
decompensate-method decompensate a flowFrame
description 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
description<--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-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-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-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"
estimateLogicle Computes a transform using the 'logicle_transform' function
estimateMedianLogicle Estimates a common logicle transformation for a flowSet.
eval-method Class "EHtrans"
eval-method Class "asinht"
eval-method Class asinhtGml2
eval-method Class "compensatedParameter"
eval-method Class "dg1polynomial"
eval-method Class "exponential"
eval-method Class filterReference
eval-method Class "hyperlog"
eval-method Class hyperlogtGml2
eval-method Class "invsplitscale"
eval-method Class lintGml2
eval-method Class "logarithm"
eval-method Class logicletGml2
eval-method Class logtGml2
eval-method Class "quadratic"
eval-method Class "ratio"
eval-method Class "ratiotGml2"
eval-method Class "sinht"
eval-method Class "splitscale"
eval-method Class "squareroot"
eval-method Class "transformReference"
eval-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-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<--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
FCSTransTransform Computes a transform using the 'iplogicle' function
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-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
filter Filter FCS files
filter,flowFrame,norm2Filter Filter FCS files
filter,flowFrame,polygonGate Filter FCS files
filter,flowFrame,rectangleGate Filter FCS files
filter-class A class for representing filtering operations to be applied to flow data.
filter-method A class for representing filtering operations to be applied to flow data.
filter-method Filter FCS files
filter-on-methods Methods for Function %on% in Package 'flowCore'
filterDetails Obtain details about a filter operation
filterDetails-method Obtain details about a filter operation
filterDetails-methods Obtain details about a filter operation
filterDetails<- Obtain details about a filter operation
filterDetails<--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-class Class filterReference
filterReference-method Class filterReference
filterReference-method Class filterSet(deprecated)
filterResult Class "filterResult"
filterResult-class Class "filterResult"
filterResultList Class "filterResultList"
filterResultList-class Class "filterResultList"
filters Class "filters" and "filtersList"
filters-class Class "filters" and "filtersList"
filterSet Class filterSet(deprecated)
filterSet-class Class filterSet(deprecated)
filtersList Class "filters" and "filtersList"
filtersList-class Class "filters" and "filtersList"
filterSummary Class "filterSummary"
filterSummary-class Class "filterSummary"
filterSummaryList Class "filterSummaryList"
filterSummaryList-class Class "filterSummaryList"
flowCore Provides S4 data structures and basic infrastructure and functions to deal with flow cytometry data.
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-method Filter FCS files
fr_append_cols Append data columns to a flowFrame
fsApply Apply a Function over values in a flowSet
fsApply,flowSet,ANY Apply a Function over values in a flowSet
fsApply-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays

-- G --

gate Class "gateActionItem"
gate-method Class "gateActionItem"
gateActionItem Class "gateActionItem"
gateActionItem-class Class "gateActionItem"
gateView Class "gateView"
gateView-class Class "gateView"
get-method Class "fcReference" and its subclasses
get-method Class "workFlow"(deprecated)
getChannelMarker get channel and marker information from a 'flowFrame' that matches to the given keyword
getIndexSort Extract Index Sorted Data from an FCS File
getIndexSort-method Extract Index Sorted Data from an FCS File
GvHD Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)

-- H --

head-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"
hyperlogtGml2 Class hyperlogtGml2
hyperlogtGml2-class Class hyperlogtGml2

-- I --

identifier Retrieve the GUID of flowCore objects
identifier-method Class "actionItem"
identifier-method Class "compensation"
identifier-method Class "fcReference" and its subclasses
identifier-method Class "filterList"
identifier-method Class filterSet(deprecated)
identifier-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
identifier-method Retrieve the GUID of flowCore objects
identifier-method Class "normalization"
identifier-method Class "subsetting"
identifier-method Class "transformList"
identifier-method Class "view"
identifier-methods Retrieve the GUID of flowCore objects
identifier<- Retrieve the GUID of flowCore objects
identifier<--method Class "compensation"
identifier<--method Filter FCS files
identifier<--method Class "filterList"
identifier<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
identifier<--method Retrieve the GUID of flowCore objects
identifier<--method Class "normalization"
identifier<--method Class "subsetting"
identifier<--method Class "transformList"
initialize-method Class "dg1polynomial"
initialize-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
initialize-method Class "parameterFilter"
initialize-method Class "ratio"
initialize-method Class "ratiotGml2"
initialize-method Class "singleParameterTransform"
intersectFilter-class Class "setOperationFilter"
intersectFilter-method Take the intersection of two filters
inverseLogicleTransform Computes the inverse of the transform defined by the 'logicleTransform' function or the transformList generated by 'estimateLogicle' function
invsplitscale Class "invsplitscale"
invsplitscale-class Class "invsplitscale"
isFCSfile Read an FCS file
isNull Class "fcReference" and its subclasses
isNull-method Class "fcReference" and its subclasses

-- J --

journal Class "workFlow"(deprecated)
journal-method Class "workFlow"(deprecated)

-- K --

keyword Methods to retrieve keywords of a flowFrame
keyword-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<--method Methods to retrieve keywords of a flowFrame
kmeansFilter Class "kmeansFilter"
kmeansFilter-class Class "kmeansFilter"

-- L --

length-method Filter FCS files
length-method Class filterReference
length-method Class "filterSummary"
length-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
length-method Class "kmeansFilter"
length-method Class "logicalFilterResult"
length-method Class "manyFilterResult"
length-method Class "multipleFilterResult"
linearTransform Create the definition of a linear transformation function to be applied on a data set
lintGml2 Class lintGml2
lintGml2-class Class lintGml2
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"
logicletGml2 Class logicletGml2
logicletGml2-class Class logicletGml2
logicleTransform Computes a transform using the 'logicle_transform' function
logtGml2 Class logtGml2
logtGml2-class Class logtGml2
logTransform Create the definition of a log transformation function (base specified by user) to be applied on a data set
ls Class "workFlow"(deprecated)
ls-method Class "workFlow"(deprecated)

-- M --

manyFilterResult Class "manyFilterResult"
manyFilterResult-class Class "manyFilterResult"
markernames get or update the marker names
markernames-method get or update the marker names
markernames<- get or update the marker names
markernames<--method get or update the marker names
mget-method Class "workFlow"(deprecated)
multipleFilterResult Class "multipleFilterResult"
multipleFilterResult-class Class "multipleFilterResult"

-- N --

name-method Filter FCS files
names 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
names-method Class "actionItem"
names-method Class "filterResultList"
names-method Class filterSet(deprecated)
names-method Class "filterSummary"
names-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
names-method Class "logicalFilterResult"
names-method Class "manyFilterResult"
names-method Class "multipleFilterResult"
names-method Class "view"
names-method Class "workFlow"(deprecated)
names<--method Class "multipleFilterResult"
ncol-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
nodes-method Class "workFlow"(deprecated)
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-method Class "normalization"
normalizeActionItem Class "normalizeActionItem"
normalizeActionItem-class Class "normalizeActionItem"
normalizeView Class "normalizeView"
normalizeView-class Class "normalizeView"
nrow-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-class Class "parameters"
parameters-method Class "compensation"
parameters-method Class "filterResultList"
parameters-method Class "manyFilterResult"
parameters-method Class "normalization"
parameters-method Obtain information about parameters for flow cytometry objects.
parameters-method Class "ratiotGml2"
parameters-method Class "singleParameterTransform"
parameters-method Class "transformReference"
parameters<- Obtain information about parameters for flow cytometry objects.
parameters<--method Class "dg1polynomial"
parameters<--method Obtain information about parameters for flow cytometry objects.
parameterTransform-class Class "parameterTransform"
parent Class "view"
parent-method Class "actionItem"
parent-method Class "view"
pData-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
pData<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
phenoData-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
phenoData<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
plot-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
plot-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
plot-method Class "workFlow"(deprecated)
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-method Class "compensateActionItem"
print-method Class "filterSummary"
print-method Class "gateActionItem"
print-method Class "normalizeActionItem"
print-method Class "subsettingActionItem"
print-method Class "transformActionItem"
print-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-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"
ratiotGml2 Class "ratiotGml2"
ratiotGml2-class Class "ratiotGml2"
rbind2,flowSet,missing 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
rbind2-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-method Class "actionItem"
Rm-method Class "compensateActionItem"
Rm-method Class "compensateView"
Rm-method Class "fcReference" and its subclasses
Rm-method Class "gateActionItem"
Rm-method Class "gateView"
Rm-method Class "normalizeActionItem"
Rm-method Class "normalizeView"
Rm-method Class "subsettingActionItem"
Rm-method Class "subsettingView"
Rm-method Class "transformActionItem"
Rm-method Class "transformView"
Rm-method Class "view"
Rm-method Class "workFlow"(deprecated)

-- S --

sampleFilter Class "sampleFilter"
sampleFilter-class Class "sampleFilter"
sampleNames-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
sampleNames<--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-method Class "boundaryFilter"
show-method Class "compensateActionItem"
show-method Class "compensation"
show-method Class "ellipsoidGate"
show-method Class "expressionFilter"
show-method Class "fcReference" and its subclasses
show-method Filter FCS files
show-method Class "filterList"
show-method Class filterReference
show-method Class "filterResult"
show-method Class "filterResultList"
show-method Class filterSet(deprecated)
show-method Class "filterSummary"
show-method Class "filters" and "filtersList"
show-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
show-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
show-method Class "gateActionItem"
show-method Class "kmeansFilter"
show-method Class "manyFilterResult"
show-method Class "multipleFilterResult"
show-method Class "norm2Filter"
show-method Class "normalizeActionItem"
show-method Class "polygonGate"
show-method Define filter boundaries
show-method Class "quadGate"
show-method Class "rectangleGate"
show-method Class "sampleFilter"
show-method Class "setOperationFilter"
show-method Class "subsetting"
show-method Class "subsettingActionItem"
show-method Class "timeFilter"
show-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
show-method Class "transformActionItem"
show-method A class for encapsulating a filter to be performed on transformed parameters
show-method A class for mapping transforms between parameters
show-method Class "unitytransform"
show-method Class "view"
show-method Class "workFlow"(deprecated)
singleParameterTransform-class Class "singleParameterTransform"
sinht Class "sinht"
sinht-class Class "sinht"
sort-method Class filterSet(deprecated)
spillover Compute a spillover matrix from a flowSet
spillover-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
spillover-method Compute a spillover matrix from a flowSet
spillover_ng Compute a spillover matrix from a flowSet, simplified API
spillover_ng-method Compute a spillover matrix from a flowSet, simplified API
split Methods to split flowFrames and flowSets according to filters
split-method Class "filterResultList"
split-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,flowSet,ANY Subset a flowFrame or a flowSet
Subset-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-method Methods for function summarizeFilter
summarizeFilter-methods Methods for function summarizeFilter
summary-method Filter FCS files
summary-method Class filterReference
summary-method Class "filterResultList"
summary-method Class "filterSummary"
summary-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
summary-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
summary-method Class "gateActionItem"
summary-method Class "gateView"
summary-method Class "logicalFilterResult"
summary-method Class "manyFilterResult"
summary-method Class "multipleFilterResult"
summary-method Class "rectangleGate"
summary-method Class "setOperationFilter"
summary-method 'transform': a class for transforming flow-cytometry data by applying scale factors.
summary-method Class "workFlow"(deprecated)

-- T --

tail-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"
toTable Class "filterSummary"
toTable-method Class "filterSummary"
toTable-method Class "filterSummaryList"
transform '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.
transform-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
transform-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
transform-method '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"(deprecated)
tree-method Class "workFlow"(deprecated)
truncateTransform Create the definition of a truncate transformation function to be applied on a data set

-- U --

undo Class "workFlow"(deprecated)
unionFilter-class Class "setOperationFilter"
unitytransform Class "unitytransform"
unitytransform-class Class "unitytransform"
updateTransformKeywords modify description to reflect the transformation Involve inserting/updating 'transformation' and flowCore_$PnRmax keywords

-- V --

validFilters Check if all filters in a filters matches same paramters
varLabels-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varLabels<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varMetadata-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
varMetadata<--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"(deprecated)
views-method Class "workFlow"(deprecated)

-- W --

workFlow Class "workFlow"(deprecated)
workFlow-class Class "workFlow"(deprecated)
write.FCS Write an FCS file
write.flowSet Write an FCS file

-- X --

xyplot-method Class "gateView"
xyplot-method Class "view"

-- misc --

!-method A class for representing filtering operations to be applied to flow data.
$-method Class "filterSummary"
$-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
$-method Class "workFlow"(deprecated)
$.flowFrame 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
%&% Take the intersection of two filters
%&%-method Take the intersection of two filters
%&%-methods Take the intersection of two filters
%in% Filter-specific membership methods
%in%-method Filter-specific membership methods
%in%-methods Filter-specific membership methods
%on% Methods for Function %on% in Package 'flowCore'
%on%-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%-method Take the intersection of two filters
%subset%-method Class filterSet(deprecated)
&-method Take the intersection of two filters
*-method Class "rectangleGate"
<-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
<=-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
==-method Class "filterResult"
==-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
>-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
>=-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
[-method Class "filterResultList"
[-method Class filterSet(deprecated)
[-method 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
[-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[-method Class "multipleFilterResult"
[-method Class "rectangleGate"
[-method Class "workFlow"(deprecated)
[[-method Class "filterResult"
[[-method Class "filterResultList"
[[-method Class filterSet(deprecated)
[[-method Class "filterSummary"
[[-method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
[[-method Class "logicalFilterResult"
[[-method Class "manyFilterResult"
[[-method Class "multipleFilterResult"
[[-method Class "workFlow"(deprecated)
[[<-,filterSet,missing,ANY,filter Class filterSet(deprecated)
[[<--method Class filterSet(deprecated)
[[<--method 'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
|-method A class for representing filtering operations to be applied to flow data.