tof_read_data: Read data from an .fcs/.csv file or a directory of .fcs/.csv...

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

Read data from an .fcs/.csv file or a directory of .fcs/.csv files.

Description

Read data from an .fcs/.csv file or a directory of .fcs/.csv files.

Usage

tof_read_data(path = NULL, sep = "|", panel_info = dplyr::tibble())

Arguments

path	A file path to a single file or to a directory of files. The only valid file types are .fcs files or .csv files containing high-dimensional cytometry data.
sep	Optional. 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

An [c by m+1] tibble in which each row represents a single cell (of c total in the dataset) and each column represents a high-dimensional cytometry measurement (of m total in the dataset). If more than one .fcs is read at once, the last column of the tibble ('file_name') will represent the file name of the .fcs file from which each cell was read.

See Also

Other input/output functions: tof_write_csv(), tof_write_data(), tof_write_fcs()

Examples

input_file <- dir(tidytof_example_data("aml"), full.names = TRUE)[[1]]
tof_read_data(input_file)

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