Package: flowCore 2.19.0
Mike Jiang
flowCore: flowCore: Basic structures for flow cytometry data
Provides S4 data structures and basic functions to deal with flow cytometry data.
Authors:
flowCore_2.19.0.tar.gz
flowCore_2.19.0.zip(r-4.5)flowCore_2.19.0.zip(r-4.4)flowCore_2.19.0.zip(r-4.3)
flowCore_2.19.0.tar.gz(r-4.5-noble)flowCore_2.19.0.tar.gz(r-4.4-noble)
flowCore.pdf |flowCore.html✨
flowCore/json (API)
NEWS
| # Install 'flowCore' in R: |
| install.packages('flowCore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- GvHD - Extract of a Graft versus Host Disease monitoring experiment
On BioConductor:flowCore-2.19.0(bioc 3.21)flowCore-2.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyinfrastructureflowcytometrycellbasedassayscpp
Last updated 2 months agofrom:46f519ee8d. Checks:OK: 1 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 29 2024 |
Exports:%&%%in%%on%%subset%arcsinhTransformasinhtasinhtGml2biexponentialTransformboundaryFiltercbind2char2ExpressionFiltercleanupcollapse_desccolnamescolnames<-compensatecompensatedParametercompensationCytoExploreR_.estimateLogicledecompensatedescriptiondescription<-dg1polynomialeach_coleach_rowEHtransellipsoidGateestimateLogicleestimateMedianLogicleevalexponentialexpressionFilterexprsexprs<-FCSTransTransformfeatureNamesfilterfilterDetailsfilterDetails<-filterListfilterReferencefiltersfiltersListflowFrameflowSetflowSet_to_listfr_append_colsfsApplygetChannelMarkergetIndexSortheadhyperloghyperlogtGml2identifieridentifier<-initializeinverseLogicleTransforminvsplitscaleisFCSfilekeywordkeyword<-kmeansFilterlinearTransformlintGml2lnTransformlogarithmlogicletGml2logicleTransformlogtGml2logTransformmanyFilterResultmarkernamesmarkernames<-multiRangeGatencolnormalizationnormalizenrowparametersparameters<-pDatapData<-phenoDataphenoData<-plotpolygonGatepolytopeGateprintquadGatequadraticquadraticTransformratioratiotGml2rbind2read.FCSread.FCSheaderread.flowSetrectangleGaterotate_gatesampleFiltersampleNamessampleNames<-scale_gatescaleTransformshift_gateshowsinhtspilloversplitsplitscalesplitScaleTransformsquarerootSubsetsummarizeFiltersummarytailtimeFiltertoTabletransformtransform_gatetransformListtransformReferencetruncateTransformunitytransformvarLabelsvarLabels<-varMetadatavarMetadata<-write.FCSwrite.flowSet
Dependencies:BHBiobaseBiocGenericscpp11cytolibgenericsmatrixStatsRcppRhdf5libRProtoBufLibS4Vectors
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 |
