imcExperiment {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.

Description

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.

Usage

imcExperiment(
  coordinates = matrix(1, 3, 3),
  cellIntensity = matrix(1, 3, 3),
  neighborHood = matrix(1, 3, 3),
  network = data.frame(matrix(1, 3, 3)),
  distance = matrix(1, 3, 3),
  morphology = matrix(1, 3, 3),
  uniqueLabel = rep("A", 3),
  panel = as.character(seq_len(3)),
  ROIID = data.frame(ROIID = rep("A", 3)),
  ...
)

Arguments

coordinates

matrix of spatial coordinates (x,y)

cellIntensity

matrix of counts

neighborHood

neighborhood results

network

network assignments for each cell

distance

distances for each cell, can be square

morphology

morphology features for each cell, can be square

uniqueLabel

character class each cell is assigned a uniqueLabel

panel

antibody panel rownames set to rowData

ROIID

character for ROI

...

additional arguments

Value

imcExperiment container

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)))