Package: flowCore 2.25.1

Mike Jiang

flowCore: flowCore: Basic structures for flow cytometry data

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

Authors:B Ellis [aut], Perry Haaland [aut], Florian Hahne [aut], Nolwenn Le Meur [aut], Nishant Gopalakrishnan [aut], Josef Spidlen [aut], Mike Jiang [aut, cre], Greg Finak [aut], Samuel Granjeaud [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowCore/json (API)

# Install 'flowCore' in R:

install.packages('flowCore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

curl– Easy-to-use client-side URL transfer library
openssl– Secure Sockets Layer toolkit
openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

GvHD - Extract of a Graft versus Host Disease monitoring experiment

On BioConductor:flowCore-2.25.1(bioc 3.24)flowCore-2.24.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology infrastructure flowcytometry cellbasedassays curl openssl openblas cpp

10.03 score 63 packages 2.2k scripts 109 mentions 130 exports 14 dependencies

Last updated from:4935c7bf31. Checks:12 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	402
linux-devel-arm64	WARNING	439
linux-devel-x86_64	WARNING	514
source / vignettes	OK	1089
linux-release-arm64	WARNING	439
linux-release-x86_64	WARNING	480
macos-release-arm64	WARNING	173
macos-release-x86_64	WARNING	371
macos-oldrel-arm64	WARNING	221
macos-oldrel-x86_64	WARNING	590
windows-devel	WARNING	319
windows-release	WARNING	370
windows-oldrel	WARNING	255
wasm-release	FAIL	664

Exports:%&%%in%%on%%subset%arcsinhTransform asinht asinhtGml2 biexponentialTransform boundaryFilter cbind2 char2ExpressionFilter cleanup collapse_desc colnames colnames<-compensate compensatedParameter compensation CytoExploreR_.estimateLogicle decompensate description description<-dg1polynomial each_col each_row EHtrans ellipsoidGate estimateLogicle estimateMedianLogicle eval exponential expressionFilter exprs exprs<-FCSTransTransform featureNames filter filterDetails filterDetails<-filterList filterReference filters filtersList flowFrame flowSet flowSet_to_list fr_append_cols fsApply getChannelMarker getIndexSort head hyperlog hyperlogtGml2 identifier identifier<-initialize inverseLogicleTransform invsplitscale isFCSfile keyword keyword<-kmeansFilter linearTransform lintGml2 lnTransform logarithm logicletGml2 logicleTransform logtGml2 logTransform manyFilterResult markernames markernames<-multiRangeGate ncol normalization normalize nrow parameters parameters<-pData pData<-phenoData phenoData<-plot polygonGate polytopeGate print quadGate quadratic quadraticTransform ratio ratiotGml2 rbind2 read.FCS read.FCSheader read.flowSet rectangleGate rotate_gate sampleFilter sampleNames sampleNames<-scale_gate scaleTransform shift_gate show sinht spillover split splitscale splitScaleTransform squareroot Subset summarizeFilter summary tail timeFilter toTable transform transform_gate transformList transformReference truncateTransform unitytransform varLabels varLabels<-varMetadata varMetadata<-write.FCS write.flowSet

Dependencies:BH Biobase BiocGenerics biocmake cpp11 cytolib dir.expiry filelock generics matrixStats Rcpp Rhdf5lib RProtoBufLib S4Vectors

Basic Functions for Flow Cytometry Data

Rendered fromHowTo-flowCore.Rnwusingknitr::knitr

Last update: 2021-01-23
Started: 2014-04-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
flowCore: Basic structures for flow cytometry data	flowCore-package flowCore
Create the definition of an arcsinh transformation function (base specified by user) to be applied on a data set	arcsinhTransform
Class "asinht"	asinht asinht-class eval,asinht,missing-method
Class asinhtGml2	asinhtGml2 asinhtGml2-class eval,asinhtGml2,missing-method
Compute a transform using the 'biexponential' function	biexponentialTransform
Class "boundaryFilter"	boundaryFilter boundaryFilter-class show,boundaryFilter-method
Class "characterOrNumeric"	characterOrNumeric characterOrNumeric-class
Class "characterOrParameters"	characterOrParameters characterOrParameters-class
Class "characterOrTransformation"	characterOrTransformation characterOrTransformation-class
Fix the offset when its values recorded in header and TEXT don't agree	checkOffset
Convert an object to another class	coerce coerce,call,filter-method coerce,character,filter-method coerce,complementFilter,call-method coerce,complementFilter,logical-method coerce,ellipsoidGate,polygonGate-method coerce,environment,flowSet-method coerce,factor,filterResult-method coerce,filter,call-method coerce,filter,logical-method coerce,filterReference,call-method coerce,filterReference,concreteFilter-method coerce,filterResult,logical-method coerce,filterResultList,list-method coerce,flowFrame,flowSet-method coerce,flowSet,flowFrame-method coerce,flowSet,list-method coerce,formula,filter-method coerce,intersectFiler,call-method coerce,intersectFilter,logical-method coerce,list,filterResultList-method coerce,list,flowSet-method coerce,list,transformList-method coerce,logical,filterResult-method coerce,logicalFilterResult,logical-method coerce,matrix,filterResult-method coerce,name,filter-method coerce,nullParameter,character-method coerce,numeric,filterResult-method coerce,parameters,character-method coerce,randomFilterResult,logical-method coerce,ratio,character-method coerce,rectangleGate,polygonGate-method coerce,subsetFilter,call-method coerce,subsetFilter,logical-method coerce,transform,character-method coerce,unionFilter,call-method coerce,unionFilter,logical-method coerce,unitytransform,character-method
Coerce the list of the keywords into a character Also flatten spillover matrix into a string	collapse_desc
Class "compensatedParameter"	compensatedParameter compensatedParameter-class eval,compensatedParameter,missing-method
Class "compensation"	compensate compensation compensation-class identifier,compensation-method identifier<-,compensation,character-method parameters,compensation-method show,compensation-method
Class complementFilter	complementFilter complementFilter-class show,complementFilter-method
Class "concreteFilter"	concreteFilter concreteFilter-class
Decompensate a flowFrame	decompensate decompensate,flowFrame,compensation-method decompensate,flowFrame,data.frame-method decompensate,flowFrame,matrix-method decompensate-methods
Class "dg1polynomial"	dg1polynomial dg1polynomial-class eval,dg1polynomial,missing-method initialize,dg1polynomial-method parameters<-,dg1polynomial,character-method parameters<-,dg1polynomial,parameters-method
Methods to apply functions over flowFrame margins	each_col each_col,flowFrame-method each_col-methods each_row each_row,flowFrame-method each_row-methods
Class "EHtrans"	EHtrans EHtrans-class eval,EHtrans,missing-method
Class "ellipsoidGate"	ellipsoidGate ellipsoidGate-class show,ellipsoidGate-method
Estimates a common logicle transformation for a flowSet.	estimateMedianLogicle
Class "exponential"	eval,exponential,missing-method exponential exponential-class
Class "expressionFilter"	char2ExpressionFilter expressionFilter expressionFilter-class show,expressionFilter-method
Computes a transform using the 'iplogicle' function	FCSTransTransform
Take the intersection of two filters	%&% %&%,ANY-method %&%,filter,filter-method %&%-methods %subset% %subset%,ANY-method %subset%,filter,filter-method %subset%,list,filter-method &,filter,filter-method &,filter,list-method &,list,filter-method coerce,intersectFilter,call-method filter-and-methods intersectFilter-method subsetFilter-method
A class for representing filtering operations to be applied to flow data.	!,filter-method booleanGate,filter-class decisionTreeGate,filter-class ellipsoidGate,filter-class filter,filter-method filter-class filtergate,filter-class norm2Filter,filter-class polygonGate,filter-class rectangleGate,filter-class \|,filter,filter-method \|,filter,list-method \|,list,filter-method
Filter-specific membership methods	%in% %in%,ANY,filterReference-method %in%,ANY,filterResult-method %in%,ANY,manyFilterResult-method %in%,ANY,multipleFilterResult-method %in%,flowFrame,boundaryFilter-method %in%,flowFrame,complementFilter-method %in%,flowFrame,ellipsoidGate-method %in%,flowFrame,expressionFilter-method %in%,flowFrame,filterResult-method %in%,flowFrame,intersectFilter-method %in%,flowFrame,kmeansFilter-method %in%,flowFrame,norm2Filter-method %in%,flowFrame,polygonGate-method %in%,flowFrame,polytopeGate-method %in%,flowFrame,quadGate-method %in%,flowFrame,rectangleGate-method %in%,flowFrame,sampleFilter-method %in%,flowFrame,subsetFilter-method %in%,flowFrame,timeFilter-method %in%,flowFrame,transformFilter-method %in%,flowFrame,unionFilter-method %in%-methods filter-in-methods
Filter FCS files	call,filter-method character,filter-method filter filter,flowFrame,filter-method filter,flowFrame,norm2Filter filter,flowFrame,polygonGate filter,flowFrame,rectangleGate filter,flowFrame-method filter,flowSet,filter-method filter,flowSet,filterList-method filter,flowSet,list-method filter-method filter-methods formula,filter-method identifier<-,filter,character-method length,filter-method name,filter-method show,filter-method summary,filter-method
Methods for Function %on% in Package `flowCore'	%on% %on%,ANY,flowSet-method %on%,filter,parameterTransform-method %on%,filter,transform-method %on%,filter,transformList-method %on%,parameterTransform,flowFrame-method %on%,transform,flowFrame-method %on%,transformList,flowFrame-method %on%,transformList,flowSet-method %on%-methods filter-on-methods
Obtain details about a filter operation	filterDetails filterDetails,filterResult,ANY-method filterDetails,filterResult,missing-method filterDetails-methods filterDetails<- filterDetails<-,filterResult,character,ANY-method filterDetails<-,filterResult,character,filter-method filterDetails<-,filterResult,character,setOperationFilter-method
Class "filterList"	filterList filterList-class identifier,filterList-method identifier<-,filterList,character-method show,filterList-method
Class filterReference	eval,filterReference,missing-method filterReference filterReference,environment,character-method filterReference-class length,filterReference-method show,filterReference-method summary,filterReference-method
Class "filterResult"	==,filterResult,flowFrame-method filterResult filterResult-class show,filterResult-method [[,filterResult,ANY-method
Class "filterResultList"	filterResultList filterResultList-class names,filterResultList-method parameters,filterResultList-method show,filterResultList-method split,flowSet,filterResultList-method summary,filterResultList-method [,filterResultList,ANY-method [[,filterResultList,ANY-method
Class "filters" and "filtersList"	filters filters-class filtersList filtersList-class show,filters-method show,filtersList-method
Class "filterSummary"	$,filterSummary-method coerce,filterSummary,data.frame-method filterSummary filterSummary-class length,filterSummary-method names,filterSummary-method print,filterSummary-method show,filterSummary-method summary,filterResult-method toTable toTable,filterSummary-method [[,filterSummary,character-method [[,filterSummary,numeric-method
Class "filterSummaryList"	filterSummaryList filterSummaryList-class toTable,filterSummaryList-method
'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run	$.flowFrame <,flowFrame,ANY-method <=,flowFrame,ANY-method ==,flowFrame,filterResult-method ==,flowFrame,flowFrame-method >,flowFrame,ANY-method >=,flowFrame,ANY-method cbind2,flowFrame,matrix-method cbind2,flowFrame,numeric-method colnames,flowFrame-method colnames<- colnames<-,flowFrame-method compensate,flowFrame,compensation-method compensate,flowFrame,data.frame-method compensate,flowFrame,matrix-method description description,flowFrame-method description<-,flowFrame,ANY-method description<-,flowFrame,list-method dim dim,flowFrame-method exprs exprs,flowFrame-method exprs<- exprs<-,flowFrame,ANY-method exprs<-,flowFrame,matrix-method featureNames featureNames,flowFrame-method flowFrame flowFrame-class head,flowFrame-method initialize,flowFrame-method names names,flowFrame-method ncol,flowFrame-method nrow,flowFrame-method plot,flowFrame,ANY-method plot,flowFrame-method range range,flowFrame-method show,flowFrame-method spillover spillover,flowFrame-method summary,flowFrame-method tail,flowFrame-method [,flowFrame,ANY-method [,flowFrame,filter-method [,flowFrame,filterResult-method
Convert a flowSet to a list of flowFrames	flowSet_to_list
'flowSet': a class for storing flow cytometry raw data from quantitative cell-based assays	$,flowSet-method colnames,flowSet-method colnames<-,flowSet-method compensate,flowSet,ANY-method compensate,flowSet,data.frame-method compensate,flowSet,list-method flowSet flowSet-class fsApply,flowSet-method identifier,flowSet-method identifier<-,flowSet,ANY-method length,flowSet-method pData,flowSet-method pData<-,flowSet,data.frame-method phenoData,flowSet-method phenoData<-,flowSet,ANY-method phenoData<-,flowSet,phenoData-method plot,flowSet,ANY-method plot,flowSet-method rbind2,flowFrame,flowSet-method rbind2,flowSet,flowFrame-method rbind2,flowSet,flowSet,missing-method rbind2,flowSet,flowSet-method rbind2,flowSet,missing rbind2,flowSet,missing-method sampleNames,flowSet-method sampleNames<-,flowSet,ANY-method show,flowSet-method summary,flowSet-method varLabels,flowSet-method varLabels<-,flowSet,ANY-method varLabels<-,flowSet-method varMetadata,flowSet-method varMetadata<-,flowSet,ANY-method [,flowSet,ANY-method [,flowSet-method [[,flowSet,ANY-method [[,flowSet-method [[<-,flowFrame-method [[<-,flowSet,ANY,ANY,flowFrame-method [[<-,flowSet-method
Append data columns to a flowFrame	fr_append_cols
Apply a Function over values in a flowSet	fsApply fsApply,flowSet,ANY
get channel and marker information from a 'flowFrame' that matches to the given keyword	getChannelMarker
Extract Index Sorted Data from an FCS File	getIndexSort getIndexSort,flowFrame-method getIndexSort-methods
Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)	GvHD
Class "hyperlog"	eval,hyperlog,missing-method hyperlog hyperlog-class
Class hyperlogtGml2	eval,hyperlogtGml2,missing-method hyperlogtGml2 hyperlogtGml2-class
Retrieve the GUID of flowCore objects	identifier identifier,filter-method identifier,filterReference-method identifier,filterResult-method identifier,flowFrame-method identifier,NULL-method identifier,transform-method identifier-methods identifier<- identifier<-,flowFrame,ANY-method identifier<-,flowFrame-method
Class intersectFilter	intersectFilter intersectFilter-class show,intersectFilter-method
Computes the inverse of the transform defined by the 'logicleTransform' function or the transformList generated by 'estimateLogicle' function	inverseLogicleTransform
Class "invsplitscale"	eval,invsplitscale,missing-method invsplitscale invsplitscale-class
Methods to retrieve keywords of a flowFrame	keyword keyword,flowFrame,character-method keyword,flowFrame,function-method keyword,flowFrame,list-method keyword,flowFrame,missing-method keyword,flowSet,ANY-method keyword,flowSet,list-method keyword-methods keyword<- keyword<-,flowFrame,ANY-method keyword<-,flowFrame,character-method keyword<-,flowFrame,list-method keyword<-,flowSet,list-method
Class "kmeansFilter"	kmeansFilter kmeansFilter-class length,kmeansFilter-method show,kmeansFilter-method
Create the definition of a linear transformation function to be applied on a data set	linearTransform
Class lintGml2	eval,lintGml2,missing-method lintGml2 lintGml2-class
Create the definition of a ln transformation function (natural logarthim) to be applied on a data set	lnTransform
Class "logarithm"	eval,logarithm,missing-method logarithm logarithm-class
Class "logicalFilterResult"	length,logicalFilterResult-method logicalFilterResult logicalFilterResult-class names,logicalFilterResult-method summary,logicalFilterResult-method [[,logicalFilterResult,ANY-method
Class logicletGml2	eval,logicletGml2,missing-method logicletGml2 logicletGml2-class
Computes a transform using the 'logicle_transform' function	estimateLogicle logicleTransform
Class logtGml2	eval,logtGml2,missing-method logtGml2 logtGml2-class
Create the definition of a log transformation function (base specified by user) to be applied on a data set	logTransform
Class "manyFilterResult"	as.data.frame.manyFilterResult length,manyFilterResult-method manyFilterResult manyFilterResult-class names,manyFilterResult-method parameters,manyFilterResult-method show,manyFilterResult-method summary,manyFilterResult-method [[,manyFilterResult,ANY-method [[,manyFilterResult-method
get or update the marker names	markernames markernames,flowFrame-method markernames,flowSet-method markernames<- markernames<-,flowFrame-method markernames<-,flowSet-method
Class "multipleFilterResult"	length,multipleFilterResult-method multipleFilterResult multipleFilterResult-class names,multipleFilterResult-method names<-,multipleFilterResult,ANY-method names<-,multipleFilterResult-method show,multipleFilterResult-method summary,multipleFilterResult-method [,multipleFilterResult,ANY-method [[,multipleFilterResult,ANY-method [[,multipleFilterResult-method
Class "normalization"	identifier,normalization-method identifier<-,normalization,character-method normalization normalization-class normalize normalize,flowSet,normalization-method parameters,normalization-method
Class "nullParameter"	nullParameter nullParameter-class
Class "parameterFilter"	initialize,parameterFilter-method parameterFilter-class
Class "parameters"	parameters-class
Obtain information about parameters for flow cytometry objects.	parameters parameters,filter-method parameters,filterReference-method parameters,filterResult-method parameters,flowFrame,missing-method parameters,flowFrame-method parameters,nullParameter-method parameters,parameterFilter-method parameters,parameterTransform-method parameters,ratio-method parameters,setOperationFilter-method parameters,transform-method parameters-methods parameters<- parameters<-,dg1polynomial,transform-method parameters<-,flowFrame,AnnotatedDataFrame-method parameters<-,parameterFilter,character-method parameters<-,parameterFilter,list-method parameters<-,parameterFilter,transform-method parameters<-,singleParameterTransform,character-method parameters<-,singleParameterTransform,transform-method
Class "parameterTransform"	parameterTransform parameterTransform-class
Class "polygonGate"	polygonGate polygonGate-class show,polygonGate-method
Define filter boundaries	polytopeGate polytopeGate-class show,polytopeGate-method
Class "quadGate"	quadGate quadGate-class show,quadGate-method
Class "quadratic"	eval,quadratic,missing-method quadratic quadratic-class
Create the definition of a quadratic transformation function to be applied on a data set	quadraticTransform
Class "randomFilterResult"	randomFilterResult randomFilterResult-class
Class "ratio"	eval,ratio,missing-method initialize,ratio-method ratio ratio-class
Class "ratiotGml2"	eval,ratiotGml2,missing-method initialize,ratiotGml2-method parameters,ratiotGml2-method ratiotGml2 ratiotGml2-class
Read an FCS file	cleanup isFCSfile read.FCS
Read the TEXT section of a FCS file	read.FCSheader
Read a set of FCS files	read.flowSet
Class "rectangleGate"	*,rectangleGate,rectangleGate-method rectangleGate rectangleGate-class show,rectangleGate-method summary,rectangleGate-method [,rectangleGate,ANY-method [,rectangleGate,character-method
Simplified geometric rotation of gates	rotate_gate rotate_gate.default
Class "sampleFilter"	sampleFilter sampleFilter-class show,sampleFilter-method
Simplified geometric scaling of gates	scale_gate scale_gate.default
Create the definition of a scale transformation function to be applied on a data set	scaleTransform
Class "setOperationFilter"	setOperationFilter setOperationFilter-class
Simplified geometric translation of gates	shift_gate shift_gate.default
Class "singleParameterTransform"	initialize,singleParameterTransform-method parameters,singleParameterTransform-method singleParameterTransform-class
Class "sinht"	eval,sinht,missing-method sinht sinht-class
Methods to split flowFrames and flowSets according to filters	split split,flowFrame,ANY-method split,flowFrame,character-method split,flowFrame,factor-method split,flowFrame,filter-method split,flowFrame,logicalFilterResult-method split,flowFrame,manyFilterResult-method split,flowFrame,multipleFilterResult-method split,flowFrame,numeric-method split,flowSet,ANY-method split,flowSet,character-method split,flowSet,factor-method split,flowSet,filter-method split,flowSet,filterResult-method split,flowSet,list-method split,flowSet,numeric-method split-methods
Class "splitscale"	eval,splitscale,missing-method splitscale splitscale-class
Compute the split-scale transformation describe by FL. Battye	splitScaleTransform
Class "squareroot"	eval,squareroot,missing-method squareroot squareroot-class
Subset a flowFrame or a flowSet	Subset Subset,flowFrame,filter-method Subset,flowFrame,logical-method Subset,flowFrame-method Subset,flowSet,ANY Subset,flowSet,ANY-method Subset,flowSet,filterResultList-method Subset,flowSet,list-method Subset-methods
Class subsetFilter	show,subsetFilter-method subsetFilter subsetFilter-class summary,subsetFilter-method
Methods for function summarizeFilter	summarizeFilter summarizeFilter,filterResult,filter-method summarizeFilter,filterResult,filterReference-method summarizeFilter,filterResult,parameterFilter-method summarizeFilter,filterResult,subsetFilter-method summarizeFilter,logicalFilterResult,norm2Filter-method summarizeFilter,logicalFilterResult,parameterFilter-method summarizeFilter,multipleFilterResult,parameterFilter-method summarizeFilter-methods
Class "timeFilter"	show,timeFilter-method timeFilter timeFilter-class
Transform a flowFrame or flowSet	transform transform,flowFrame-method transform,flowSet-method
Simplified geometric transformation of gates	transform_gate transform_gate.default
'transform': a class for transforming flow-cytometry data by applying scale factors.	show,transform-method summary,transform-method transform,missing-method transform-class
Class "transformation"	transformation transformation-class
A class for encapsulating a filter to be performed on transformed parameters	show,transformFilter-method transformFilter transformFilter-class
Class "transformList"	c,transformList-method colnames,transformList-method identifier,transformList-method identifier<-,transformList,character-method transformList transformList-class
A class for mapping transforms between parameters	show,transformMap-method transformMap transformMap-class
Class "transformReference"	eval,transformReference,missing-method parameters,transformReference-method transformReference transformReference-class
Create the definition of a truncate transformation function to be applied on a data set	truncateTransform
Class unionFilter	show,unionFilter-method unionFilter unionFilter-class
Class "unitytransform"	eval,unitytransform,missing-method show,unitytransform-method unitytransform unitytransform-class
modify description to reflect the transformation Involve inserting/updating 'transformation' and flowCore_$PnRmax keywords	updateTransformKeywords
Check if all filters in a filters matches same paramters	validFilters
Write an FCS file	write.FCS
Write an FCS file	write.flowSet