calculateMultiChannelAof: Calculate Average Overlap Frequency (AOF) for multiple...

In ismmshimc/cytutils: Cytometry quality control and reproducibility utilities

Calculate Average Overlap Frequency (AOF) for multiple channels of interest.

Description

Calculate the Average Overlap Frequency (AOF) for multiple cytometry channels.

Usage

calculateMultiChannelAof(channel_population_relationships_filepath,
  base_fcs_data_filepath, single_sample_labels, sample_id, cofactor = NULL)

Arguments

channel_population_relationships_filepath	Filepath of the channel population relationships csv file that outlines channels of interest as well as negative and positive populations for that channel. Column names start with "channel", followed by cell population names (i.e. "b_cell", "t_cell", etc.). Cell values are TRUE, FALSE, or left empty.
base_fcs_data_filepath	Filepath of the "base" FCS file. This file has data for all cells from the sample, regardless of manual gating population designation.
single_sample_labels	A list illustrating the relationships between specific samples, cells, and population assignments designated via manual gating. This can be generated via the 'generatePopulationAssignments' function.
sample_id	A string representing the sample ID of interest. sample_id should correspond to a key in the single_sample_labels list.
cofactor	If supplied, data will be transformed using inverse hyperbolic sin with given cofactor.

Value

A data frame with AOF values for each channel of interest, as denoted by the channel_population_relationships csv file.

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