# flowCore: Basic structures for flow cytometry data

## Documentation for package ‘flowCore’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

flowCore-package | flowCore: Basic structures for flow cytometry data

## -- A --

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

## -- 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
characterOrNumeric | Class "characterOrNumeric"
characterOrNumeric-class | Class "characterOrNumeric"
characterOrParameters | Class "characterOrParameters"
characterOrParameters-class | Class "characterOrParameters"
characterOrTransformation | Class "characterOrTransformation"
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"
collapse_desc | Coerce the list of the keywords into a character Also flatten spillover matrix into a string
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
compensatedParameter | Class "compensatedParameter"
compensatedParameter-class | Class "compensatedParameter"
compensation | Class "compensation"
compensation-class | Class "compensation"
complementFilter | Class complementFilter
complementFilter-class | Class complementFilter
concreteFilter | Class "concreteFilter"
concreteFilter-class | Class "concreteFilter"

## -- D --

decisionTreeGate,filter-class | A class for representing filtering operations to be applied to flow data.
decompensate | Decompensate a flowFrame
decompensate-method | Decompensate a flowFrame
decompensate-methods | 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 | Methods to apply functions over flowFrame margins
each_col-method | Methods to apply functions over flowFrame margins
each_col-methods | Methods to apply functions over flowFrame margins
each_row | Methods to apply functions over flowFrame margins
each_row-method | Methods to apply functions over flowFrame margins
each_row-methods | Methods 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 --

FCSTransTransform | Computes a transform using the 'iplogicle' function
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-and-methods | Take the intersection of two filters
filter-class | A class for representing filtering operations to be applied to flow data.
filter-in-methods | Filter-specific membership methods
filter-method | A class for representing filtering operations to be applied to flow data.
filter-method | Filter FCS files
filter-methods | 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
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"
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 | flowCore: Basic structures for 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
flowSet_to_list | Convert a flowSet to a list of flowFrames
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 --

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
getIndexSort-methods | 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 "compensation"
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 "transformList"
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 "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 intersectFilter
intersectFilter-class | Class intersectFilter
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

## -- 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

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

## -- 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-methods | Obtain information about parameters for flow cytometry objects.
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 "parameterTransform"
parameterTransform-class | Class "parameterTransform"
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
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 "filterSummary"

## -- 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 "randomFilterResult"
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"
rotate_gate | Simplified geometric rotation of gates
rotate_gate.default | Simplified geometric rotation of gates

## -- 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
scale_gate | Simplified geometric scaling of gates
scale_gate.default | Simplified geometric scaling of gates
setOperationFilter | Class "setOperationFilter"
setOperationFilter-class | Class "setOperationFilter"
shift_gate | Simplified geometric translation of gates
shift_gate.default | Simplified geometric translation of gates
show-method | Class "boundaryFilter"
show-method | Class "compensation"
show-method | Class complementFilter
show-method | Class "ellipsoidGate"
show-method | Class "expressionFilter"
show-method | Filter FCS files
show-method | Class "filterList"
show-method | Class filterReference
show-method | Class "filterResult"
show-method | Class "filterResultList"
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 intersectFilter
show-method | Class "kmeansFilter"
show-method | Class "manyFilterResult"
show-method | Class "multipleFilterResult"
show-method | Class "polygonGate"
show-method | Define filter boundaries
show-method | Class "quadGate"
show-method | Class "rectangleGate"
show-method | Class "sampleFilter"
show-method | Class subsetFilter
show-method | Class "timeFilter"
show-method | 'transform': a class for transforming flow-cytometry data by applying scale factors.
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 unionFilter
show-method | Class "unitytransform"
singleParameterTransform-class | Class "singleParameterTransform"
sinht | Class "sinht"
sinht-class | Class "sinht"
spillover | 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
spillover-method | 'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
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
Subset-methods | Subset a flowFrame or a flowSet
subsetFilter | Class subsetFilter
subsetFilter-class | Class subsetFilter
subsetFilter-method | Take the intersection of two filters
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 "logicalFilterResult"
summary-method | Class "manyFilterResult"
summary-method | Class "multipleFilterResult"
summary-method | Class "rectangleGate"
summary-method | Class subsetFilter
summary-method | 'transform': a class for transforming flow-cytometry data by applying scale factors.

## -- 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 flowFrame or flowSet
transform-class | 'transform': a class for transforming flow-cytometry data by applying scale factors.
transform-method | 'transform': a class for transforming flow-cytometry data by applying scale factors.
transform-method | Transform a flowFrame or flowSet
transformation | Class "transformation"
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"
transform_gate | Simplified geometric transformation of gates
transform_gate.default | Simplified geometric transformation of gates
truncateTransform | Create the definition of a truncate transformation function to be applied on a data set

## -- U --

unionFilter | Class unionFilter
unionFilter-class | Class unionFilter
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

## -- W --

write.FCS | Write an FCS file
write.flowSet | Write an FCS file

## -- 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
$.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
&-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 | '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 "filterResult"
[[-method | Class "filterResultList"
[[-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 | '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.