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flowCore

Core flow infrastructure

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Version

Version

1.32.2

License

Artistic-2.0

Maintainer

MJiang

Last Published

February 15th, 2017

Functions in flowCore (1.32.2)

compensateActionItem-class

Class "compensateActionItem"

concreteFilter-class

Class "concreteFilter"

compensatedParameter-class

Class "compensatedParameter"

Method to apply functions over flowFrame margins

filterSummary-class

Class "filterSummary"

Create the definition of a ln transformation function (natural logarthim) to be applied on a data set

filterSummaryList-class

Class "filterSummaryList"

biexponentialTransform

Compute a transform using the 'biexponential' function

norm2Filter-class

Class "norm2Filter"

logicalFilterResult-class

Class "logicalFilterResult"

normalization-class

Class "normalization"

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

setOperationFilter-class

Class "setOperationFilter"

Compute a spillover matrix from a flowSet

Methods to split flowFrames and flowSets according to filters

boundaryFilter-class

Class "boundaryFilter"

ellipsoidGate-class

Class "ellipsoidGate"

expressionFilter-class

Class "expressionFilter"

filterDetails-methods

Obtain details about a filter operation

Methods for Function %on% in Package `flowCore'

Extract Index Sorted Data from an FCS File

getChannelMarker

get channel and marker information from a flowFrame that matches to the given keyword

manyFilterResult-class

Class "manyFilterResult"

polygonGate-class

Class "polygonGate"

multipleFilterResult-class

Class "multipleFilterResult"

polytopeGate-class

Define filter boundaries

Class "quadGate"

transformView-class

Class "transformView"

Class "workFlow"(deprecated)

truncateTransform

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

Write an FCS file

quadraticTransform

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

singleParameterTransform-class

Class "singleParameterTransform"

unitytransform-class

Class "unitytransform"

compensateView-class

Class "compensateView"

compensation-class

Class "compensation"

fcReference-class

Class "fcReference" and its subclasses

FCSTransTransform

Computes a transform using the 'iplogicle' function

filterList-class

Class "filterList"

filterReference-class

Class filterReference

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

Retrieve the GUID of flowCore objects

Obtain information about parameters for flow cytometry objects.

parameterTransform-class

Class "parameterTransform"

randomFilterResult-class

Class "randomFilterResult"

Read an FCS file

subsettingView-class

Class "subsettingView"

summarizeFilter-methods

Methods for function summarizeFilter

transformFilter-class

A class for encapsulating a filter to be performed on transformed parameters

transformList-class

Class "transformList"

characterOrTransformation-class

Class "characterOrTransformation"

Convert an object to another class

filter-and-methods

Take the intersection of two filters

A class for representing filtering operations to be applied to flow data.

filterResult-class

Class "filterResult"

filterResultList-class

Class "filterResultList"

Apply a Function over values in a flowSet

'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays

logicleTransform

Computes a transform using the 'logicle_transform' function

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

normalizeActionItem-class

Class "normalizeActionItem"

normalizeView-class

Class "normalizeView"

rectangleGate-class

Class "rectangleGate"

transformActionItem-class

Class "transformActionItem"

sampleFilter-class

Class "sampleFilter"

actionItem-class

Class "actionItem"

arcsinhTransform

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

filterSet-class

Class filterSet(deprecated)

Class "filters" and "filtersList"

Class "gateView"

inverseLogicleTransform

Computes the inverse of the transform defined by the 'logicleTransform' function

gateActionItem-class

Class "gateActionItem"

keyword-methods

Methods to retrieve keywords of a flowFrame

subsetting-class

Class "subsetting"

timeFilter-class

Class "timeFilter"

subsettingActionItem-class

Class "subsettingActionItem"

transform-class

'transform': a class for transforming flow-cytometry data by applying scale factors.

transformation-class

Class "transformation"

filter-in-methods

Filter-specific membership methods

Filter FCS files

flowCore-package

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

flowFrame-class

'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

linearTransform

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

kmeansFilter-class

Class "kmeansFilter"

parameterFilter-class

Class "parameterFilter"

Read the TEXT section of a FCS file

parameters-class

Class "parameters"

Read a set of FCS files

splitScaleTransform

Compute the split-scale transformation describe by FL. Battye

Subset a flowFrame or a flowSet

transformMap-class

A class for mapping transforms between parameters

transformReference-class

Class "transformReference"

Write an FCS file