readFCS {IFC} | R Documentation |
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), space = list(at = 6, n =
4), 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, text_check = FALSE, text_empty = FALSE,
text_trim = "none"),
display_progress = TRUE,
...
)
Arguments
fileName |
path to file. |
options |
list of options used to parse FCS file. It should contain (otherwise, it will be filled with the default values listed below): |
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.
'options' members with the exception of 'header' may be passed thanks to '...'.
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-value pairs
- text, list of keywords values,
- data, data.frame of values.
Source
Data File Standard for Flow Cytometry, version FCS 3.1 from Spidlen J. et al. available at doi: 10.1002/cyto.a.20825.