Function reference • flowCore

Data: Classes Classes for managing the data from one or more cytometry datasets (FCS files).
`flowFrame-class`	'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
`flowSet-class`	'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
`coerce`	Convert an object to another class
`flowSet_to_list()`	Convert a flowSet to a list of flowFrames
Data: Methods Methods for accessing the data and metadata associated with flowFrame or flowSet objects.
`Subset()`	Subset a flowFrame or a flowSet
`each_col()` `each_row()`	Methods to apply functions over flowFrame margins
`fr_append_cols()`	Append data columns to a flowFrame
`getIndexSort`	Extract Index Sorted Data from an FCS File
`fsApply()`	Apply a Function over values in a flowSet
`identifier()`	Retrieve the GUID of flowCore objects
`markernames()` `markernames<-`()	get or update the marker names
`getChannelMarker()`	get channel and marker information from a `flowFrame` that matches to the given keyword
`parameters()`	Obtain information about parameters for flow cytometry objects.
`keyword()`	Methods to retrieve keywords of a flowFrame
Reading/writing data Methods for reading/writing cytometry data and metadata from FCS files to/from flowCore data structures.
`isFCSfile()` `read.FCS()`	Read an FCS file
`read.FCSheader()`	Read the TEXT section of a FCS file
`read.flowSet()`	Read a set of FCS files
`collapse_desc()`	Coerce the list of the keywords into a character Also flatten spillover matrix into a string
`write.FCS()`	Write an FCS file
`write.flowSet()`	Write an FCS file
Compensation Classes to represent compensation to be applied to raw cytometry data and methods to apply them.
`compensation()` `compensate()`	Class "compensation"
`decompensate(<flowFrame>,<matrix>)` `decompensate(<flowFrame>,<compensation>)`	Decompensate a flowFrame
`compensatedParameter-class`	Class "compensatedParameter"
Filters: Classes Classes representing general filters applied to cytometry data and methods to create them.
`filter-class`	A class for representing filtering operations to be applied to flow data.
`concreteFilter-class`	Class "concreteFilter"
`transformFilter-class`	A class for encapsulating a filter to be performed on transformed parameters
`expressionFilter()` `char2ExpressionFilter()`	Class "expressionFilter"
`parameterFilter-class`	Class "parameterFilter"
`filterList()`	Class "filterList"
`filters()` `filtersList()`	Class "filters" and "filtersList"
`filterResult-class`	Class "filterResult"
`filterResultList-class`	Class "filterResultList"
`summary(<filterResult>)`	Class "filterSummary"
`filterSummaryList-class`	Class "filterSummaryList"
`filterReference-class`	Class filterReference
`filterDetails-methods`	Obtain details about a filter operation
`timeFilter()`	Class "timeFilter"
`boundaryFilter()`	Class "boundaryFilter"
`kmeansFilter()`	Class "kmeansFilter"
`unionFilter-class`	Class unionFilter
`intersectFilter-class`	Class intersectFilter
`complementFilter-class`	Class complementFilter
`subsetFilter-class`	Class subsetFilter
`setOperationFilter-class`	Class "setOperationFilter"
`sampleFilter()`	Class "sampleFilter"
`logicalFilterResult-class`	Class "logicalFilterResult"
`randomFilterResult-class`	Class "randomFilterResult"
`manyFilterResult-class`	Class "manyFilterResult"
Filters: Methods Methods for applying filters, accessing information about them, and logically combining them.
`%&%` `%subset%`	Take the intersection of two filters
`%in%`	Filter-specific membership methods
`%on%`	Methods for Function %on% in Package `flowCore'
`filter()`	Filter FCS files
`split-methods`	Methods to split flowFrames and flowSets according to filters
`summarizeFilter()`	Methods for function summarizeFilter
Gates: Classes Classes representing geometric gates (which are themselves filter objects). Note that gates are applied to data in the same way as other filters.
`rectangleGate()`	Class "rectangleGate"
`quadGate()`	Class "quadGate"
`polygonGate()`	Class "polygonGate"
`polytopeGate()`	Define filter boundaries
`ellipsoidGate()`	Class "ellipsoidGate"
Gates: Methods Methods for applying simple geometric manipulations to gates.
`transform_gate(<default>)`	Simplified geometric transformation of gates
`scale_gate(<default>)`	Simplified geometric scaling of gates
`shift_gate(<default>)`	Simplified geometric translation of gates
`rotate_gate(<default>)`	Simplified geometric rotation of gates
Transformations Classes for representing transformations to be applied to cytometry data in analysis and methods for generating them, interacting with them, and applying them.
`transform(<flowFrame>)`	Transform a flowFrame or flowSet
`transform-class`	'transform': a class for transforming flow-cytometry data by applying scale factors.
`transformList()`	Class "transformList"
`transformMap-class`	A class for mapping transforms between parameters
`transformReference-class`	Class "transformReference"
`parameterTransform-class`	Class "parameterTransform"
`unitytransform-class`	Class "unitytransform"
`scaleTransform()`	Create the definition of a scale transformation function to be applied on a data set
`truncateTransform()`	Create the definition of a truncate transformation function to be applied on a data set
`dg1polynomial-class`	Class "dg1polynomial"
`ratio-class`	Class "ratio"
`ratiotGml2-class`	Class "ratiotGml2"
`linearTransform()`	Create the definition of a linear transformation function to be applied on a data set
`lintGml2-class`	Class lintGml2
`squareroot-class`	Class "squareroot"
`quadratic-class`	Class "quadratic"
`quadraticTransform()`	Create the definition of a quadratic transformation function to be applied on a data set
`exponential-class`	Class "exponential"
`logarithm-class`	Class "logarithm"
`logTransform()`	Create the definition of a log transformation function (base specified by user) to be applied on a data set
`logtGml2-class`	Class logtGml2
`hyperlog-class`	Class "hyperlog"
`hyperlogtGml2-class`	Class hyperlogtGml2
`lnTransform()`	Create the definition of a ln transformation function (natural logarthim) to be applied on a data set
`splitscale-class`	Class "splitscale"
`splitScaleTransform()`	Compute the split-scale transformation describe by FL. Battye
`invsplitscale-class`	Class "invsplitscale"
`sinht-class`	Class "sinht"
`asinht-class`	Class "asinht"
`arcsinhTransform()`	Create the definition of an arcsinh transformation function (base specified by user) to be applied on a data set
`asinhtGml2-class`	Class asinhtGml2
`biexponentialTransform()`	Compute a transform using the 'biexponential' function
`EHtrans-class`	Class "EHtrans"
`logicleTransform()` `estimateLogicle()`	Computes a transform using the 'logicle_transform' function
`FCSTransTransform()`	Computes a transform using the 'iplogicle' function
`logicletGml2-class`	Class logicletGml2
`estimateMedianLogicle()`	Estimates a common logicle transformation for a flowSet.
`inverseLogicleTransform()`	Computes the inverse of the transform defined by the 'logicleTransform' function or the transformList generated by 'estimateLogicle' function
`normalization()` `normalize()`	Class "normalization"
Data Datasets included for use in examples to illustrate flowCore functionality
`GvHD`	Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)

Reference

Data: Classes

Data: Methods

Reading/writing data

Compensation

Filters: Classes

Filters: Methods

Gates: Classes

Gates: Methods

Transformations

Data