greedyCytometryAof: Greedy search for optimal Average Overlap Frequency (AOF)...

In ismmshimc/cytutils: Cytometry quality control and reproducibility utilities

Greedy search for optimal Average Overlap Frequency (AOF) values.

Description

Given a cytometry data matrix and its clustering scheme, use a greedy search strategy to find a partition of clusters that minimizes the AOF for each marker.

Usage

greedyCytometryAof(fcs_data, y, channel_names = colnames(fcs_data),
  width = 0.05, cofactor = NULL, verbose = TRUE)

Arguments

fcs_data	A numerical matrix (NxD) of acquired cytometry data. Each row corresponds to a cell, each column to a channel.
y	A factor vector of length N which includes the cluster assignment of each cell.
channel_names	A character vector which lists the columns (channels) in fcs_data for which to calculate the AOF.
width	Width of high threshold of negative population and low threshold of positive population.
cofactor	If supplied, data will be transformed using inverse hyperbolic sin with given cofactor.
verbose	Boolean. Should the function report progress to terminal.

Value

A data frame with AOF values for each channel.

ismmshimc/cytutils documentation built on Aug. 26, 2022, 2:07 p.m.