{
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  "Package": "imcExperiment",
  "Title": "Mass Cytometry S4 Class Structure Pipeline for Images",
  "Version": "0.99.0",
  "Authors@R": "person(\"Anthony\", \"Colombo\", email = \"anthonycolombo60@gmail.com\", role=c(\"aut\",\"cre\"))",
  "Maintainer": "Anthony Colombo <anthonycolombo60@gmail.com>",
  "Description": "Containerizes cytometry data and allows for S4 class\nstructure to extend slots related to cell morphology, spatial\ncoordinates, phenotype network information, and unique cellular\nlabeling.",
  "License": "MIT + file LICENSE",
  "biocViews": "Software, WorkflowStep, MultipleComparison",
  "Encoding": "UTF-8",
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  "Repository": "https://arcolombo.r-universe.dev",
  "Date/Publication": "2021-08-18 17:40:39 UTC",
  "RemoteUrl": "https://github.com/arcolombo/imcexperiment",
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  "Packaged": {
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    "User": "root"
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  "Author": "Anthony Colombo [aut, cre]",
  "_user": "arcolombo",
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    "workflowstep",
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    "cellIntensity",
    "cellIntensity<-",
    "getCoordinates",
    "getCoordinates<-",
    "getDistance",
    "getDistance<-",
    "getLabel",
    "getMorphology",
    "getMorphology<-",
    "getNeighborhood",
    "getNeighborhood<-",
    "getNetwork",
    "getNetwork<-",
    "imcExperiment",
    "imcExperimentToHyperFrame",
    "percentilenormalize",
    "selectCases",
    "subsetCase"
  ],
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      "name": "data",
      "title": "data",
      "object": "data",
      "file": "data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ImageId",
        "CellId",
        "marker1",
        "marker2",
        "marker3",
        "marker4",
        "marker5",
        "marker6",
        "marker7",
        "marker8",
        "marker9",
        "marker10",
        "marker11",
        "marker12",
        "marker13",
        "marker14",
        "marker15",
        "marker16",
        "marker17",
        "marker18",
        "marker19",
        "marker20",
        "marker21",
        "marker22",
        "marker23",
        "marker24",
        "marker25",
        "marker26",
        "marker27",
        "marker28",
        "marker29",
        "marker30",
        "marker31",
        "marker32",
        "marker33",
        "marker34",
        "Area",
        "Eccentricity",
        "Solidity",
        "Extent",
        "EulerNumber",
        "Perimeter",
        "MajorAxisLength",
        "MinorAxisLength",
        "Orientation",
        "X_position",
        "Y_position",
        "Percent_Touching",
        "Number_Neighbors",
        "neighbour_4_CellId1",
        "neighbour_4_CellId2",
        "neighbour_4_CellId3",
        "neighbour_4_CellId4",
        "neighbour_4_CellId5",
        "neighbour_4_CellId6",
        "neighbour_4_CellId7",
        "neighbour_4_CellId8",
        "neighbour_4_CellId9",
        "neighbour_4_CellId10",
        "Phenograph7851534969",
        "tSNE4148542692_1",
        "tSNE4148542692_2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "imcdata",
      "title": "imcdata",
      "object": "imcData",
      "file": "imcData.rda",
      "class": [
        "imcExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "dot-checkSpatialDimension",
      "title": "the rows are the panel names, the columns are the single cells,the column are the single cells to match the SCE designs (scRNA)",
      "topics": [
        ".checkSpatialDimension"
      ]
    },
    {
      "page": "dot-imcExperimentToPPP",
      "title": "map to point pattern from imcExperiment class.",
      "topics": [
        ".imcExperimentToPPP"
      ]
    },
    {
      "page": "cellIntensity",
      "title": "finds the intensities getter.",
      "topics": [
        "cellIntensity",
        "cellIntensity,imcExperiment-method",
        "cellIntensity<-",
        "cellIntensity<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "data",
      "title": "data",
      "topics": [
        "data"
      ]
    },
    {
      "page": "getCoordinates",
      "title": "finds the spatial coords, getter.",
      "topics": [
        "getCoordinates",
        "getCoordinates,imcExperiment-method",
        "getCoordinates<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "getCoordinates-set",
      "title": "Sets the coordinate positions of each cell (matrix), columns are X,Y positions.",
      "topics": [
        "getCoordinates<-"
      ]
    },
    {
      "page": "getDistance-set",
      "title": "re-assigns the distance matrix (rows are cells)",
      "topics": [
        "getDistance<-"
      ]
    },
    {
      "page": "getMorphology-set",
      "title": "re-assigns morphological features can be stored (matrix) rows are cells and columns are Area, etc.",
      "topics": [
        "getMorphology<-"
      ]
    },
    {
      "page": "getNeighborhood",
      "title": "finds the neighborhood information.",
      "topics": [
        "getNeighborhood",
        "getNeighborhood,imcExperiment-method",
        "getNeighborhood<-",
        "getNeighborhood<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "getNetwork-set",
      "title": "re-assigns the network assignment (matrix)",
      "topics": [
        "getNetwork<-"
      ]
    },
    {
      "page": "imcdata",
      "title": "imcdata",
      "topics": [
        "imcdata"
      ]
    },
    {
      "page": "imcExperiment",
      "title": "Initializes a imcExperiment and performs some rudimentary checks. Many of the arguments CAN be NULL; determination of which is required is done at run-time.  A imcExperiment must contain at least the expressions and spatial/coordinate assays.",
      "topics": [
        "imcExperiment"
      ]
    },
    {
      "page": "imcExperiment-class",
      "title": "a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'",
      "topics": [
        ".imcExperiment",
        "getDistance",
        "getDistance,imcExperiment-method",
        "getDistance<-,imcExperiment,matrix-method",
        "getLabel",
        "getLabel,imcExperiment-method",
        "getMorphology",
        "getMorphology,imcExperiment-method",
        "getMorphology<-,imcExperiment,matrix-method",
        "getNetwork",
        "getNetwork,imcExperiment-method",
        "getNetwork<-,imcExperiment,data.frame-method",
        "imcExperiment-class",
        "imcExperiment-method",
        "spatial"
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    {
      "page": "imcExperimentToHyperFrame",
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      "topics": [
        "imcExperimentToHyperFrame"
      ]
    },
    {
      "page": "percentilenormalize",
      "title": "given a matrix of intensity counts, perform min/max norm.",
      "topics": [
        "percentilenormalize"
      ]
    },
    {
      "page": "selectCases",
      "title": "subsets the imcExperiment to a case along with all slots for a selected multiple ROIs.",
      "topics": [
        "selectCases",
        "selectCases,imcExperiment-method"
      ]
    },
    {
      "page": "subsetCase",
      "title": "subsets the imcExperiment to a case along with all slots for a single ROI, using for distance analysis",
      "topics": [
        "subsetCase",
        "subsetCase,imcExperiment-method"
      ]
    }
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    "Biobase",
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    "generics",
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    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "polyclip",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
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    "spatstat.univar",
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      "title": "imcExperiment: containerization of IMC data",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "PCA demo analysis",
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        "Access unique cell ID",
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        "IMC and flowSet conversions",
        "Diffcyt package tutorial (extra)"
      ],
      "created": "2020-03-03 16:43:58",
      "modified": "2021-08-18 17:06:22",
      "commits": 11
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