tof_read_file: Read high-dimensional cytometry data from a single .fcs or...

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Read high-dimensional cytometry data from a single .fcs or .csv file into a tidy tibble.

Description

Read high-dimensional cytometry data from a single .fcs or .csv file into a tidy tibble.

Usage

tof_read_file(file_path = NULL, sep = "|", panel_info = dplyr::tibble())

Arguments

file_path	A file path to a single .fcs or .csv file.
sep	A string to use to separate the antigen name and its associated metal in the column names of the output tibble. Defaults to "|". Only used if the input file is an .fcs file.
panel_info	Optional. A tibble or data.frame containing information about the panel used during high-dimensional cytometry data acquisition. Two columns are required: "metals" and "antigens". Only used if the input file is a .csv file.

Value

A 'tof_tbl' in which each row represents a single cell and each column represents a high-dimensional cytometry antigen channel.

A 'tof_tbl' is an S3 class that extends the "tibble" class by storing one additional attribute: "panel" (a tibble storing information about the panel used during data acquisition). Because panel information isn't obvious from data read as a .csv file, this information must be provided manually by the user.

keyes-timothy/tidytof documentation built on Aug. 28, 2024, 8:37 a.m.