# Mass Cytometry S4 Class Structure Pipeline for Images

## 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