read.FCS, this takes a filename for a single
FCS file and returns a
load_cytoframe_from_fcs( filename, transformation = "linearize", which.lines = NULL, alter.names = FALSE, column.pattern = NULL, invert.pattern = FALSE, decades = 0, is_h5 = NULL, backend = get_default_backend(), uri = NULL, h5_filename = NULL, min.limit = NULL, truncate_max_range = TRUE, dataset = NULL, emptyValue = TRUE, num_threads = 1, ignore.text.offset = FALSE, text.only = FALSE )
The filename of the single FCS file to be read
A character string that defines the type of
transformation. Valid values are
Numeric vector to specify the indices of the lines to be
read. If it is NULL, all the records are read. If it is of length 1, a random sample of
the size indicated by
Logical indicating whether or not we should rename the
columns to valid R names using
An optional regular expression defining parameters we should keep when loading the file. The default is NULL.
Logical. By default,
When scaling is activated, the number of decades to use for the output.
Logical indicating whether the data should be stored in h5 format
String specifying a name for the h5 file if
The minimum value in the data range that is allowed. Some
instruments produce extreme artifactual values. The positive data range for
each parameter is completely defined by the measurement range of the
instrument and all larger values are set to this threshold. The lower data
boundary is not that well defined, since compensation might shift some
values below the original measurement range of the instrument. This can be
set to an arbitrary number or to
Logical. Default is TRUE. can be optionally turned off to avoid truncating the extreme positive value to the instrument measurement range, i.e. '$PnR'.
The FCS file specification allows for multiple data segments
in a single file. Since the output of
Logical indicating whether or not to allow empty values for keywords in TEXT segment. It affects how double delimiters are treated. If TRUE, double delimiters are parsed as a pair of start and end single delimiters for an empty value. Otherwise, double delimiters are parsed as one part of the string of the keyword value. The default is TRUE.
Integer allowing for parallelization of the parsing operation by specifiying a number of threads
Logical indicating whether to ignore the keyword values in TEXT segment when they don't agree with the HEADER. Default is FALSE, which throws the error when such a discrepancy is found. Users can turn it on to ignore the TEXT segment when they are sure of the accuracy of the HEADER segment so that the file still can be read.
whether to only parse text section of FCS (default is FALSE), it is sometime useful to skip loading data section for the faster loading meta data from FCS
An object of class
cytoframe that contains the data, the parameters monitored,
and the keywords and values saved in the header of the FCS file.
load_cytoframe_from_fcs works with the output of the FACS machine
software from a number of vendors (FCS 2.0, FCS 3.0 and List Mode Data LMD).
However, the FCS 3.0 standard includes some options that are not yet
implemented in this function. If you need extensions, please let us know.
The output of the function is an object of class
which.lines arguments allow you to read a subset of the record as
you might not want to read the thousands of events recorded in the FCS file.
It is mainly used when there is not enough memory to read one single FCS
(which probably will not happen). It will probably take more time than
reading the entire FCS (due to the multiple disk IO).