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"[[<-,flowFrame-method", "[[<-,flowSet,ANY,ANY,flowFrame-method", "[[<-,flowSet-method" ] }, { "page": "fr_append_cols", "title": "Append data columns to a flowFrame", "topics": [ "fr_append_cols" ] }, { "page": "fsApply", "title": "Apply a Function over values in a flowSet", "topics": [ "fsApply", "fsApply,flowSet,ANY" ] }, { "page": "getChannelMarker", "title": "get channel and marker information from a 'flowFrame' that matches to the given keyword", "topics": [ "getChannelMarker" ] }, { "page": "getIndexSort", "title": "Extract Index Sorted Data from an FCS File", "topics": [ "getIndexSort", "getIndexSort,flowFrame-method", "getIndexSort-methods" ] }, { "page": "GvHD", "title": "Extract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)", "topics": [ "GvHD" ] }, { "page": "hyperlog-class", "title": "Class \"hyperlog\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,hyperlog,missing-method", "hyperlog", "hyperlog-class" ] }, { "page": "hyperlogtGml2-class", "title": "Class hyperlogtGml2", "concept": [ "mathematical transform classes" ], "topics": [ "eval,hyperlogtGml2,missing-method", "hyperlogtGml2", "hyperlogtGml2-class" ] }, { "page": "identifier-methods", "title": "Retrieve the GUID of flowCore objects", "topics": [ "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" ] }, { "page": "intersectFilter-class", "title": "Class intersectFilter", "concept": [ "setOperationFilter classes" ], "topics": [ "intersectFilter", "intersectFilter-class", "show,intersectFilter-method" ] }, { "page": "inverseLogicleTransform", "title": "Computes the inverse of the transform defined by the 'logicleTransform' function or the transformList generated by 'estimateLogicle' function", "concept": [ "Transform functions" ], "topics": [ "inverseLogicleTransform" ] }, { "page": "invsplitscale-class", "title": "Class \"invsplitscale\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,invsplitscale,missing-method", "invsplitscale", "invsplitscale-class" ] }, { "page": "keyword-methods", "title": "Methods to retrieve keywords of a flowFrame", "topics": [ "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" ] }, { "page": "kmeansFilter-class", "title": "Class \"kmeansFilter\"", "topics": [ "kmeansFilter", "kmeansFilter-class", "length,kmeansFilter-method", "show,kmeansFilter-method" ] }, { "page": "linearTransform", "title": "Create the definition of a linear transformation function to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "linearTransform" ] }, { "page": "lintGml2-class", "title": "Class lintGml2", "concept": [ "mathematical transform classes" ], "topics": [ "eval,lintGml2,missing-method", "lintGml2", "lintGml2-class" ] }, { "page": "lnTransform", "title": "Create the definition of a ln transformation function (natural logarthim) to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "lnTransform" ] }, { "page": "logarithm-class", "title": "Class \"logarithm\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,logarithm,missing-method", "logarithm", "logarithm-class" ] }, { "page": "logicalFilterResult-class", "title": "Class \"logicalFilterResult\"", "topics": [ "length,logicalFilterResult-method", "logicalFilterResult", "logicalFilterResult-class", "names,logicalFilterResult-method", "summary,logicalFilterResult-method", "[[,logicalFilterResult,ANY-method" ] }, { "page": "logicletGml2-class", "title": "Class logicletGml2", "concept": [ "mathematical transform classes" ], "topics": [ "eval,logicletGml2,missing-method", "logicletGml2", "logicletGml2-class" ] }, { "page": "logicleTransform", "title": "Computes a transform using the 'logicle_transform' function", "concept": [ "Transform functions" ], "topics": [ "estimateLogicle", "logicleTransform" ] }, { "page": "logtGml2-class", "title": "Class logtGml2", "concept": [ "mathematical transform classes" ], "topics": [ "eval,logtGml2,missing-method", "logtGml2", "logtGml2-class" ] }, { "page": "logTransform", "title": "Create the definition of a log transformation function (base specified by user) to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "logTransform" ] }, { "page": "manyFilterResult-class", "title": "Class \"manyFilterResult\"", "topics": [ "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" ] }, { "page": "markernames", "title": "get or update the marker names", "topics": [ "markernames", "markernames,flowFrame-method", "markernames,flowSet-method", "markernames<-", "markernames<-,flowFrame-method", "markernames<-,flowSet-method" ] }, { "page": "multipleFilterResult-class", "title": "Class \"multipleFilterResult\"", "topics": [ "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" ] }, { "page": "normalization-class", "title": "Class \"normalization\"", "topics": [ "identifier,normalization-method", "identifier<-,normalization,character-method", "normalization", "normalization-class", "normalize", "normalize,flowSet,normalization-method", "parameters,normalization-method" ] }, { "page": "nullParameter-class", "title": "Class \"nullParameter\"", "topics": [ "nullParameter", "nullParameter-class" ] }, { "page": "parameterFilter-class", "title": "Class \"parameterFilter\"", "topics": [ "initialize,parameterFilter-method", "parameterFilter-class" ] }, { "page": "parameters-class", "title": "Class \"parameters\"", "topics": [ "parameters-class" ] }, { "page": "parameters-methods", "title": "Obtain information about parameters for flow cytometry objects.", "topics": [ "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" ] }, { "page": "parameterTransform-class", "title": "Class \"parameterTransform\"", "topics": [ "parameterTransform", "parameterTransform-class" ] }, { "page": "polygonGate-class", "title": "Class \"polygonGate\"", "concept": [ "Gate classes" ], "topics": [ "polygonGate", "polygonGate-class", "show,polygonGate-method" ] }, { "page": "polytopeGate-class", "title": "Define filter boundaries", "concept": [ "Gate classes" ], "topics": [ "polytopeGate", "polytopeGate-class", "show,polytopeGate-method" ] }, { "page": "quadGate-class", "title": "Class \"quadGate\"", "concept": [ "Gate classes" ], "topics": [ "quadGate", "quadGate-class", "show,quadGate-method" ] }, { "page": "quadratic-class", "title": "Class \"quadratic\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,quadratic,missing-method", "quadratic", "quadratic-class" ] }, { "page": "quadraticTransform", "title": "Create the definition of a quadratic transformation function to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "quadraticTransform" ] }, { "page": "randomFilterResult-class", "title": "Class \"randomFilterResult\"", "topics": [ "randomFilterResult", "randomFilterResult-class" ] }, { "page": "ratio-class", "title": "Class \"ratio\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,ratio,missing-method", "initialize,ratio-method", "ratio", "ratio-class" ] }, { "page": "ratiotGml2-class", "title": "Class \"ratiotGml2\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,ratiotGml2,missing-method", "initialize,ratiotGml2-method", "parameters,ratiotGml2-method", "ratiotGml2", "ratiotGml2-class" ] }, { "page": "read.FCS", "title": "Read an FCS file", "topics": [ "cleanup", "isFCSfile", "read.FCS" ] }, { "page": "read.FCSheader", "title": "Read the TEXT section of a FCS file", "topics": [ "read.FCSheader" ] }, { "page": "read.flowSet", "title": "Read a set of FCS files", "topics": [ "read.flowSet" ] }, { "page": "rectangleGate-class", "title": "Class \"rectangleGate\"", "concept": [ "Gate classes" ], "topics": [ "*,rectangleGate,rectangleGate-method", "rectangleGate", "rectangleGate-class", "show,rectangleGate-method", "summary,rectangleGate-method", "[,rectangleGate,ANY-method", "[,rectangleGate,character-method" ] }, { "page": "rotate_gate", "title": "Simplified geometric rotation of gates", "topics": [ "rotate_gate", "rotate_gate.default" ] }, { "page": "sampleFilter-class", "title": "Class \"sampleFilter\"", "topics": [ "sampleFilter", "sampleFilter-class", "show,sampleFilter-method" ] }, { "page": "scale_gate", "title": "Simplified geometric scaling of gates", "topics": [ "scale_gate", "scale_gate.default" ] }, { "page": "scaleTransform", "title": "Create the definition of a scale transformation function to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "scaleTransform" ] }, { "page": "setOperationFilter-class", "title": "Class \"setOperationFilter\"", "concept": [ "setOperationFilter classes" ], "topics": [ "setOperationFilter", "setOperationFilter-class" ] }, { "page": "shift_gate", "title": "Simplified geometric translation of gates", "topics": [ "shift_gate", "shift_gate.default" ] }, { "page": "singleParameterTransform-class", "title": "Class \"singleParameterTransform\"", "topics": [ "initialize,singleParameterTransform-method", "parameters,singleParameterTransform-method", "singleParameterTransform-class" ] }, { "page": "sinht-class", "title": "Class \"sinht\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,sinht,missing-method", "sinht", "sinht-class" ] }, { "page": "split-methods", "title": "Methods to split flowFrames and flowSets according to filters", "topics": [ "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" ] }, { "page": "splitscale-class", "title": "Class \"splitscale\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,splitscale,missing-method", "splitscale", "splitscale-class" ] }, { "page": "splitScaleTransform", "title": "Compute the split-scale transformation describe by FL. Battye", "concept": [ "Transform functions" ], "topics": [ "splitScaleTransform" ] }, { "page": "squareroot-class", "title": "Class \"squareroot\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,squareroot,missing-method", "squareroot", "squareroot-class" ] }, { "page": "Subset-methods", "title": "Subset a flowFrame or a flowSet", "topics": [ "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" ] }, { "page": "subsetFilter-class", "title": "Class subsetFilter", "concept": [ "setOperationFilter classes" ], "topics": [ "show,subsetFilter-method", "subsetFilter", "subsetFilter-class", "summary,subsetFilter-method" ] }, { "page": "summarizeFilter-methods", "title": "Methods for function summarizeFilter", "topics": [ "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" ] }, { "page": "timeFilter-class", "title": "Class \"timeFilter\"", "topics": [ "show,timeFilter-method", "timeFilter", "timeFilter-class" ] }, { "page": "transform", "title": "Transform a flowFrame or flowSet", "topics": [ "transform", "transform,flowFrame-method", "transform,flowSet-method" ] }, { "page": "transform_gate", "title": "Simplified geometric transformation of gates", "topics": [ "transform_gate", "transform_gate.default" ] }, { "page": "transform-class", "title": "'transform': a class for transforming flow-cytometry data by applying scale factors.", "topics": [ "show,transform-method", "summary,transform-method", "transform,missing-method", "transform-class" ] }, { "page": "transformation-class", "title": "Class \"transformation\"", "topics": [ "transformation", "transformation-class" ] }, { "page": "transformFilter-class", "title": "A class for encapsulating a filter to be performed on transformed parameters", "topics": [ "show,transformFilter-method", "transformFilter", "transformFilter-class" ] }, { "page": "transformList-class", "title": "Class \"transformList\"", "topics": [ "c,transformList-method", "colnames,transformList-method", "identifier,transformList-method", "identifier<-,transformList,character-method", "transformList", "transformList-class" ] }, { "page": "transformMap-class", "title": "A class for mapping transforms between parameters", "topics": [ "show,transformMap-method", "transformMap", "transformMap-class" ] }, { "page": "transformReference-class", "title": "Class \"transformReference\"", "topics": [ "eval,transformReference,missing-method", "parameters,transformReference-method", "transformReference", "transformReference-class" ] }, { "page": "truncateTransform", "title": "Create the definition of a truncate transformation function to be applied on a data set", "concept": [ "Transform functions" ], "topics": [ "truncateTransform" ] }, { "page": "unionFilter-class", "title": "Class unionFilter", "concept": [ "setOperationFilter classes" ], "topics": [ "show,unionFilter-method", "unionFilter", "unionFilter-class" ] }, { "page": "unitytransform-class", "title": "Class \"unitytransform\"", "concept": [ "mathematical transform classes" ], "topics": [ "eval,unitytransform,missing-method", "show,unitytransform-method", "unitytransform", "unitytransform-class" ] }, { "page": "updateTransformKeywords", "title": "modify description to reflect the transformation Involve inserting/updating 'transformation' and flowCore_$PnRmax keywords", "topics": [ "updateTransformKeywords" ] }, { "page": "validFilters", "title": "Check if all filters in a filters matches same paramters", "topics": [ "validFilters" ] }, { "page": "write.FCS", "title": "Write an FCS file", "topics": [ "write.FCS" ] }, { "page": "write.flowSet", "title": "Write an FCS file", "topics": [ "write.flowSet" ] } ], "_readme": "https://github.com/bioc/flowCore/raw/HEAD/README.md", "_rundeps": [ "BH", "Biobase", "BiocGenerics", "biocmake", "cpp11", "cytolib", "dir.expiry", "filelock", "generics", "matrixStats", "Rcpp", "Rhdf5lib", "RProtoBufLib", "S4Vectors" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libcrypto", "package": "libssl3t64", "headers": "libssl-dev", "source": "openssl", "version": "3.0.13-0ubuntu3.9", "name": "openssl", "homepage": "https://www.openssl.org/", "description": "Secure Sockets Layer toolkit - 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