readFCS: FCS File Parser

Description

Parse data from Flow Cytometry Standard (FCS) compliant files.

Usage

readFCS(
  fileName,
  options = list(header = list(start = list(at = 0, n = 6), text_beg = list(at = 10, n
    = 8), text_end = list(at = 18, n = 8), data_beg = list(at = 26, n = 8), data_end =
    list(at = 34, n = 8)), apply_scale = TRUE, dataset = 1, force_header = FALSE,
    text_only = FALSE),
  display_progress = TRUE,
  ...
)

Value

a list whose elements are lists for each dataset stored within the file.

each sub-list contains:

- header, list of header information corresponding to 'options'

- delimiter, unique character used to separate keyword - values

- text, list of keywords values,

- data, data.frame of values.

Arguments

fileName: path to file.
options: list of options used to parse FCS file. It should contain:
- header, a list whose members define the "at" offset from header$start$at and the "n" number of bytes to extract:
-- start: where start reading FCS dataset. Default is list(at = 0, n = 6),
-- text_beg: where to retrieve file text segment beginning. Default is list(at = 10, n = 8),
-- text_end: where to retrieve file text segment end. Default is list(at = 18, n = 8),
-- data_beg: where to retrieve file text segment beginning. Default is list(at = 26, n = 8),
-- data_end: where to retrieve file text segment end. Default is list(at = 34, n = 8),
- apply_scale, whether to apply data scaling. It only applies when fcs file is stored as DATATYPE "I". Default is TRUE.
- dataset, (coerced to) an ordered vector of unique indices of desired dataset(s) to extract. Default is 1 to extract only the first dataset, whereas NULL allows to extract all available datasets.
- force_header, whether to force the use of header to determine the position of data segment. Default is FALSE, for using positions found in "$BEGINDATA" and "$ENDDATA" keywords.
- text_only, whether to only extract text segment. Default is FALSE.
display_progress: whether to display a progress bar. Default is TRUE.
...: other arguments to be passed.

Details

'options' may be tweaked according to file type, instrument and software used to generate it.
Default 'options' should allow to read most files.
'apply_scale', 'force_header', 'dataset', and 'textt_only' can also be passed to 'options' thanks to ...