imcExperiment-class {imcExperiment}

a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'

Description

a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'

finds the network information.

assigns cell cluster assignment to the container. rows are cells and column is the cluster ID

finds the distance information.

distance matrix can be stored in the distance slot for pairwise distance

finds the morphology information.

morphological features can be stored (matrix) rows are cells and columns are Area, etc.

finds the label information.

unique cell labels can be assigned (vector)

Usage

getNetwork(object)

## S4 method for signature 'imcExperiment'
getNetwork(object)

## S4 replacement method for signature 'imcExperiment,data.frame'
getNetwork(object) <- value

getDistance(object)

## S4 method for signature 'imcExperiment'
getDistance(object)

## S4 replacement method for signature 'imcExperiment,matrix'
getDistance(object) <- value

getMorphology(object)

## S4 method for signature 'imcExperiment'
getMorphology(object)

## S4 replacement method for signature 'imcExperiment,matrix'
getMorphology(object) <- value

getLabel(object)

## S4 method for signature 'imcExperiment'
getLabel(object)

Arguments

object

imcExperiment

value

matrix rows cells, columns are Area, etc.

Value

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

imcExperiment container

Slots

coordinates

matrix class containing x,y coordinates

cellIntensity

matrix class containing intensity

neighborHood

matrix class containing x,y neighbor

network

data frame class containing network

distance

matrix class containing x,y distances

morphology

matrix class containing morphology

uniqueLabel

labels

Examples

x<-imcExperiment(cellIntensity=matrix(1,nrow=10,ncol=10),
coordinates=matrix(1,nrow=10,ncol=2),
neighborHood=matrix(1,nrow=10,ncol=10),
network=data.frame(matrix(1,nrow=10,ncol=10)),
distance=matrix(1,nrow=10,ncol=10),
morphology=matrix(1,nrow=10,ncol=10),
uniqueLabel=paste0("A",seq_len(10)),
panel=letters[1:10],
ROIID=data.frame(ROIID=rep("A",10)))
data(imcdata)
getNetwork(imcdata)
data(imcdata)
getNetwork(imcdata)
data(imcdata)
x<-data.frame(ID=seq_len(ncol(imcdata)))
getNetwork(imcdata)<-x
data(imcdata)
getDistance(imcdata)
data(imcdata)
getDistance(imcdata)
data(imcdata)
newD<-matrix(1,nrow=ncol(imcdata),ncol=1)
getDistance(imcdata)<-newD
data(imcdata)
getMorphology(imcdata)
data(imcdata)
getMorphology(imcdata)
data(imcdata)
x<-matrix(1,nrow=ncol(imcdata),ncol=4)
getMorphology(imcdata)<-x
data(imcdata)
getLabel(imcdata)
data(imcdata)
getLabel(imcdata)