imcExperiment (version 0.99.0)

imcExperiment-class: 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 imcExperiment
getNetwork(object)
# S4 method for imcExperiment,data.frame
getNetwork(object) <- value
getDistance(object)
# S4 method for imcExperiment
getDistance(object)
# S4 method for imcExperiment,matrix
getDistance(object) <- value
getMorphology(object)
# S4 method for imcExperiment
getMorphology(object)
# S4 method for imcExperiment,matrix
getMorphology(object) <- value
getLabel(object)
# S4 method for 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

# NOT RUN {
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)
# }