Parse data from Flow Cytometry Standard (FCS) compliant files.
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, first_only = TRUE),
display_progress = TRUE,
...
)path to file.
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. Default is TRUE - first_only, whether to extract only first. Default is FALSE
whether to display a progress bar. Default is TRUE.
other arguments to be passed.
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.
'options' may be tweaked according to file type, instrument and software used to generate it. Default 'options' should allow to read most files.