Skip to contents

Extract the average expression for all markers for each cell type in each region defined by lisaClust

Source: R/Statial.R
getMarkerMeans.Rd

Takes a SingleCellExperiment and outputs a dataframe in a convenient format for cross validation

Usage

getMarkerMeans(
  data,
  imageID = NULL,
  cellType = NULL,
  region = NULL,
  markers = NULL,
  assay = 1,
  replaceVal = 0
)

Arguments

data

A SingleCellExperiment object with intensities data in the assays slot and regions information in colData generated by lisaClust.

imageID

The colData column that stores the image IDs.

cellType

The colData column that store the cell types.

region

The colData column that stores the regions.

markers

A string vector of markers that proxy a cell's state. If NULL, all markers will be used.

assay

Which assay do you want to use for the expression data.

replaceVal

A value to replace missing values with.

Examples

data(kerenSCE)

kerenSCE <- kerenSCE[,kerenSCE$imageID %in% c("5","6")]

regionSCE <- lisaClust::lisaClust(kerenSCE, k = 5)
#> Generating local L-curves. If you run out of memory, try 'fast = FALSE'.

lisaClustOutput <- getMarkerMeans(regionSCE)