imcExperiment: Initializes a imcExperiment and performs some rudimentary...

In imcExperiment: Mass Cytometry S4 Class Structure Pipeline for Images

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)))

imcExperiment documentation built on Aug. 19, 2021, 5:07 p.m.