cellCounts {cytofast}R Documentation

Extract cell counts from cfList

Description

A function to add the frequency (or abundance) of cell clusters per sample to a cfList.

Usage

cellCounts(cfList, frequency = FALSE, scale = FALSE)

Arguments

cfList

a cfList object. It should contain at least data in the 'expr' slot.

frequency

one of

  • a logical value. if FALSE, the abundance of the cell counts are used. If TRUE, the frequency of the total amount of given cells is used.

  • a numeric vector of same length as amount of samples

scale

a logical value. Do the cell frequencies need to be centered and scaled? The default scale function is called.

Value

Returns a cfList with a 'counts' slot.

Examples

# Read Data
dirFCS <- system.file("extdata", package="cytofast")
cfData <- readCytosploreFCS(dir = dirFCS, colNames = "description")

# Add cell counts to cfList
cfData <- cellCounts(cfData)
[Package cytofast version 1.3.0 Index]