cellCounts: Extract cell counts from cfList

In cytofast: cytofast - A quick visualization and analysis tool for CyTOF data

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)

cytofast documentation built on Nov. 8, 2020, 5:46 p.m.