Mass Cytometry S4 Class Structure Pipeline for Images

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Documentation for package ‘imcExperiment’ version 0.99.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.checkSpatialDimension	the rows are the panel names, the columns are the single cells,the column are the single cells to match the SCE designs (scRNA)
.imcExperiment	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
.imcExperimentToPPP	map to point pattern from imcExperiment class.
cellIntensity	finds the intensities getter.
cellIntensity-method	finds the intensities getter.
cellIntensity<-	finds the intensities getter.
cellIntensity<--method	finds the intensities getter.
data	data
getCoordinates	finds the spatial coords, getter.
getCoordinates-method	finds the spatial coords, getter.
getCoordinates<-	Sets the coordinate positions of each cell (matrix), columns are X,Y positions.
getCoordinates<--method	finds the spatial coords, getter.
getDistance	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getDistance-method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getDistance<-	re-assigns the distance matrix (rows are cells)
getDistance<--method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getLabel	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getLabel-method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getMorphology	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getMorphology-method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getMorphology<-	re-assigns morphological features can be stored (matrix) rows are cells and columns are Area, etc.
getMorphology<--method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getNeighborhood	finds the neighborhood information.
getNeighborhood-method	finds the neighborhood information.
getNeighborhood<-	finds the neighborhood information.
getNeighborhood<--method	finds the neighborhood information.
getNetwork	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getNetwork-method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
getNetwork<-	re-assigns the network assignment (matrix)
getNetwork<--method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
imcdata	imcdata
imcExperiment	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.
imcExperiment-class	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
imcExperiment-method	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
imcExperimentToHyperFrame	map to point pattern from imcExperiment class.
percentilenormalize	given a matrix of intensity counts, perform min/max norm.
selectCases	subsets the imcExperiment to a case along with all slots for a selected multiple ROIs.
selectCases-method	subsets the imcExperiment to a case along with all slots for a selected multiple ROIs.
spatial	a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'
subsetCase	subsets the imcExperiment to a case along with all slots for a single ROI, using for distance analysis
subsetCase-method	subsets the imcExperiment to a case along with all slots for a single ROI, using for distance analysis