generatePopulationAssignments: Generate population assignments for manually gated data

In ismmshimc/cytutils: Cytometry quality control and reproducibility utilities

Generate population assignments for manually gated data

Description

Generate a list with keys representing sample IDs (ex: sample_1, sample_2). Values are data frames with columns representing cell populations (ex: sample_1.basophil, sample_1.b_cell). Data frame cell values are booleans.

Usage

generatePopulationAssignments(manual_labeling_filepath, samples_filepath,
  data_dir)

Arguments

manual_labeling_filepath	Path to csv file with columns representing sample_id, base, and manually gated populations. Each row contains a sample_id as well as the corresponding base FCS filename and FCS files for manually gating populations. Note: The base FCS file contains data for all cells from the sample, regardless of manual gating population designation
samples_filepath	Filepath of the samples csv file that outlines sample IDs and corresponding FCS file paths.
data_dir	Path to directory containing all FCS files.

Value

A list illustrating the relationships between specific samples, cells, and population assignments designated via manual gating.

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