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flowCore
Core flow infrastructure
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Version
Version
1.38.2
1.36.0
1.34.11
1.32.2
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Version
1.38.2
License
Artistic-2.0
Maintainer
MJiang
Last Published
January 1st, 1970
Functions in flowCore (1.38.2)
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compensatedParameter-class
Class "compensatedParameter"
compensateView-class
Class "compensateView"
estimateMedianLogicle
Estimates a common logicle transformation for a flowSet.
gateView-class
Class "gateView"
%on%
Methods for Function %on% in Package `flowCore'
expressionFilter-class
Class "expressionFilter"
gateActionItem-class
Class "gateActionItem"
filterDetails-methods
Obtain details about a filter operation
lnTransform
Create the definition of a ln transformation function (natural logarthim) to be applied on a data set
logicalFilterResult-class
Class "logicalFilterResult"
markernames
get or update the marker names
transformList-class
Class "transformList"
transformMap-class
A class for mapping transforms between parameters
manyFilterResult-class
Class "manyFilterResult"
write.FCS
Write an FCS file
workFlow-class
Class "workFlow"(deprecated)
actionItem-class
Class "actionItem"
arcsinhTransform
Create the definition of an arcsinh transformation function (base specified by user) to be applied on a data set
filters-class
Class "filters" and "filtersList"
filterSet-class
Class filterSet(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
quadGate-class
Class "quadGate"
polytopeGate-class
Define filter boundaries
setOperationFilter-class
Class "setOperationFilter"
summarizeFilter-methods
Methods for function summarizeFilter
singleParameterTransform-class
Class "singleParameterTransform"
timeFilter-class
Class "timeFilter"
truncateTransform
Create the definition of a truncate transformation function to be applied on a data set
unitytransform-class
Class "unitytransform"
filter-and-methods
Take the intersection of two filters
biexponentialTransform
Compute a transform using the 'biexponential' function
each_col
Method to apply functions over flowFrame margins
boundaryFilter-class
Class "boundaryFilter"
filter-in-methods
Filter-specific membership methods
filter-class
A class for representing filtering operations to be applied to flow data.
flowFrame-class
'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
filter
Filter FCS files
flowCore-package
Provides S4 data structures and basic infrastructure and functions to deal with flow cytometry data.
logicleTransform
Computes a transform using the 'logicle_transform' function
logTransform
Create the definition of a log transformation function (base specified by user) to be applied on a data set
multipleFilterResult-class
Class "multipleFilterResult"
parameterTransform-class
Class "parameterTransform"
norm2Filter-class
Class "norm2Filter"
Subset
Subset a flowFrame or a flowSet
polygonGate-class
Class "polygonGate"
filterReference-class
Class filterReference
ellipsoidGate-class
Class "ellipsoidGate"
filterList-class
Class "filterList"
fsApply
Apply a Function over values in a flowSet
flowSet-class
'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays
GvHD
Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)
identifier
Retrieve the GUID of flowCore objects
parameters-class
Class "parameters"
parameters
Obtain information about parameters for flow cytometry objects.
read.FCS
Read an FCS file
read.FCSheader
Read the TEXT section of a FCS file
sampleFilter-class
Class "sampleFilter"
subsetting-class
Class "subsetting"
subsettingActionItem-class
Class "subsettingActionItem"
subsettingView-class
Class "subsettingView"
write.flowSet
Write an FCS file
scaleTransform
Create the definition of a scale transformation function to be applied on a data set
transformReference-class
Class "transformReference"
transformView-class
Class "transformView"
coerce
Convert an object to another class
compensateActionItem-class
Class "compensateActionItem"
fcReference-class
Class "fcReference" and its subclasses
FCSTransTransform
Computes a transform using the 'iplogicle' function
filterResult-class
Class "filterResult"
filterResultList-class
Class "filterResultList"
kmeansFilter-class
Class "kmeansFilter"
linearTransform
Create the definition of a linear transformation function to be applied on a data set
normalization-class
Class "normalization"
normalizeActionItem-class
Class "normalizeActionItem"
quadraticTransform
Create the definition of a quadratic transformation function to be applied on a data set
randomFilterResult-class
Class "randomFilterResult"
split-methods
Methods to split flowFrames and flowSets according to filters
splitScaleTransform
Compute the split-scale transformation describe by FL. Battye
transformation-class
Class "transformation"
transformFilter-class
A class for encapsulating a filter to be performed on transformed parameters
validFilters
Check if all filters in a filters matches same paramters
view-class
Class "view"
characterOrTransformation-class
Class "characterOrTransformation"
checkOffset
Fix the offset when its values recorded in header and TEXT don't agree
compensation-class
Class "compensation"
concreteFilter-class
Class "concreteFilter"
filterSummary-class
Class "filterSummary"
filterSummaryList-class
Class "filterSummaryList"
inverseLogicleTransform
Computes the inverse of the transform defined by the 'logicleTransform' function
normalizeView-class
Class "normalizeView"
keyword-methods
Methods to retrieve keywords of a flowFrame
parameterFilter-class
Class "parameterFilter"
read.flowSet
Read a set of FCS files
rectangleGate-class
Class "rectangleGate"
sinht-class
Class "sinht"
transform-class
'transform': a class for transforming flow-cytometry data by applying scale factors.
spillover
Compute a spillover matrix from a flowSet
transformActionItem-class
Class "transformActionItem"