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  "Description": "Provides HDF5 storage based methods and functions for\nmanipulation of flow cytometry data.",
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    "clone.ncdfFlowSet",
    "colnames",
    "colnames<-",
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    "filter",
    "getFileName",
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    "initIndices",
    "keyword",
    "keyword<-",
    "lapply",
    "load_ncfs",
    "markernames",
    "markernames<-",
    "ncdfFlowList",
    "ncdfFlowSet",
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    "pData",
    "pData<-",
    "phenoData",
    "phenoData<-",
    "rbind2",
    "read.ncdfFlowSet",
    "sampleNames<-",
    "save_ncfs",
    "split",
    "Subset",
    "transform",
    "unlink",
    "updateIndices"
  ],
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    {
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      "title": "subsetting by sampleNames,channels(not for events) methods",
      "topics": [
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        "[,ncdfFlowSet,ANY-method"
      ]
    },
    {
      "page": "extractFlowFrame",
      "title": "extract a 'flowFrame' object from 'ncdfFlowSet'",
      "topics": [
        "[[,ncdfFlowList,character,missing-method",
        "[[,ncdfFlowList,character-method",
        "[[,ncdfFlowList,logical-method",
        "[[,ncdfFlowList,numeric-method",
        "[[,ncdfFlowSet,ANY-method"
      ]
    },
    {
      "page": "as.flowSet",
      "title": "convert from a 'ncdfFlowSet' to a 'flowSet'",
      "topics": [
        "as.flowSet"
      ]
    },
    {
      "page": "clone.ncdfFlowSet",
      "title": "Clone a ncdfFlowSet",
      "topics": [
        "clone.ncdfFlowSet"
      ]
    },
    {
      "page": "flowSet-accessor",
      "title": "Accessors compatible with those for 'flowSet'",
      "topics": [
        "colnames,ncdfFlowList-method",
        "colnames<-",
        "colnames<-,ncdfFlowList-method",
        "colnames<-,ncdfFlowSet,ANY-method",
        "colnames<-,ncdfFlowSet-method",
        "compensate,flowSet,data.frame-method",
        "compensate,ncdfFlowSet,ANY-method",
        "compensate,ncdfFlowSet,list-method",
        "filter,ncdfFlowList,filter-method",
        "filter,ncdfFlowList,filterList-method",
        "filter,ncdfFlowList,list-method",
        "keyword,ncdfFlowSet,list-method",
        "keyword<-,ncdfFlowSet,list-method",
        "length,ncdfFlowList-method",
        "markernames,ncdfFlowList-method",
        "markernames<-,ncdfFlowList-method",
        "pData,ncdfFlowList-method",
        "pData<-,ncdfFlowList,data.frame-method",
        "phenoData,ncdfFlowList-method",
        "phenoData<-,ncdfFlowList,AnnotatedDataFrame-method",
        "sampleNames,ncdfFlowList-method",
        "sampleNames<-",
        "sampleNames<-,ncdfFlowSet,ANY-method",
        "transform,ncdfFlowSet-method"
      ]
    },
    {
      "page": "getFileName",
      "title": "get the cdf file name associated with ncdfFlowSet object",
      "topics": [
        "getFileName"
      ]
    },
    {
      "page": "Indices",
      "title": "'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet",
      "topics": [
        "getIndices",
        "getIndices,ncdfFlowSet,character-method",
        "initIndices",
        "initIndices,ncdfFlowSet-method",
        "updateIndices",
        "updateIndices,ncdfFlowSet,character,logical-method"
      ]
    },
    {
      "page": "lapply-methods",
      "title": "lapply method for ncdfFlowList",
      "topics": [
        "lapply,ncdfFlowList-method"
      ]
    },
    {
      "page": "ncdfFlow",
      "title": "ncdfFlow: A package that provides CDF storage based flow cytometry data analysis.",
      "topics": [
        "ncdfFlow"
      ]
    },
    {
      "page": "ncdfFlowList-class",
      "title": "a class that stores multiple ncdfFlowSet objects",
      "topics": [
        "ncdfFlowList",
        "ncdfFlowList-class",
        "show,ncdfFlowList-method"
      ]
    },
    {
      "page": "ncdfFlowSet-class",
      "title": "a class for storing flow cytometry raw data in HDF5 format",
      "topics": [
        "ncdfFlowSet-class",
        "show",
        "show,ncdfFlowSet-method"
      ]
    },
    {
      "page": "ncdfFlowSet-constructor",
      "title": "create ncdfFlowSet from flowSet",
      "topics": [
        "ncdfFlowSet",
        "ncdfFlowSet,flowSet-method"
      ]
    },
    {
      "page": "ncfsApply-ncdfFlowSet-method",
      "title": "apply method for ncdfFlowSet (for internal use)",
      "topics": [
        "ncfsApply",
        "ncfsApply,ncdfFlowSet-method"
      ]
    },
    {
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      "title": "combine multiple ncdfFlowSet objects into one",
      "topics": [
        "rbind2,ncdfFlowList,ANY-method"
      ]
    },
    {
      "page": "read.ncdfFlowSet",
      "title": "create ncdfFlowSet from FCS files",
      "topics": [
        "read.ncdfFlowSet",
        "read.ncdfFlowset"
      ]
    },
    {
      "page": "replacement-method-for-ncdfFlowSet",
      "title": "write the flow data from a 'flowFrame' to 'ncdfFlowSet' flowFrame can have less channels than ncdfFlowSet,which is used for partial updating(useful for 'normalization')",
      "topics": [
        "replacement method for ncdfFlowSet",
        "[[<-,ncdfFlowSet,ANY,ANY,flowFrame-method",
        "[[<-,ncdfFlowSet,flowFrame-method"
      ]
    },
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      "title": "save/load a ncdfFlowSet object to/from disk.",
      "topics": [
        "load_ncfs",
        "save_ncfs"
      ]
    },
    {
      "page": "ncdfFlowSet-split",
      "title": "split a 'ncdfFlowSet' object.",
      "topics": [
        "split,ncdfFlowList,character-method",
        "split,ncdfFlowList,factor-method",
        "split,ncdfFlowSet,character-method",
        "split,ncdfFlowSet,factor-method",
        "split,ncdfFlowSet,filter-method",
        "split,ncdfFlowSet,filterResultList-method",
        "split,ncdfFlowSet,list-method"
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    },
    {
      "page": "ncdfFlowSet-Subset",
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      "topics": [
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        "Subset,ncdfFlowList,filterResultList-method",
        "Subset,ncdfFlowSet,filter-method",
        "Subset,ncdfFlowSet,filterResultList-method",
        "Subset,ncdfFlowSet,list-method"
      ]
    },
    {
      "page": "subset-functions",
      "title": "subset the ncdfFlowSet/ncdfFlowList based on 'pData'",
      "topics": [
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        "subset.ncdfFlowSet"
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    {
      "page": "unlink-ncdfFlowSet-method",
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      "topics": [
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      ]
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