load_cytoframe_from_fcs: Read a single FCS file in to a cytoframe

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

Similar to read.FCS, this takes a filename for a single FCS file and returns a cytoframe.

Usage

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
)

Arguments

filename	The filename of the single FCS file to be read
transformation	A character string that defines the type of transformation. Valid values are linearize (default), linearize-with-PnG-scaling, or scale. The linearize transformation applies the appropriate power transform to the data. The linearize-with-PnG-scaling transformation applies the appropriate power transform for parameters stored on log scale, and also a linear scaling transformation based on the "gain" (FCS $PnG keywords) for parameters stored on a linear scale. The scale transformation scales all columns to [0,10^{decades}]. defaulting to decades=0 as in the FCS4 specification. A logical can also be used: TRUE is equal to linearize and FALSE(or NULL) corresponds to no transformation. Also, when the transformation keyword of the FCS header is set to "custom" or "applied", no transformation will be used.
which.lines	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 which.lines is read in.
alter.names	Logical indicating whether or not we should rename the columns to valid R names using make.names. The default is FALSE.
column.pattern	An optional regular expression defining parameters we should keep when loading the file. The default is NULL.
invert.pattern	Logical. By default, FALSE. If TRUE, inverts the regular expression specified in column.pattern. This is useful for indicating the channel names that we do not want to read. If column.pattern is set to NULL, this argument is ignored.
decades	When scaling is activated, the number of decades to use for the output.
is_h5	Logical indicating whether the data should be stored in h5 format
h5_filename	String specifying a name for the h5 file if is_h5 is TRUE
min.limit	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 NULL (the default value), in which case the original values are kept.
truncate_max_range	Logical. Default is TRUE. can be optionally turned off to avoid truncating the extreme positive value to the instrument measurement range, i.e. '$PnR'.
dataset	The FCS file specification allows for multiple data segments in a single file. Since the output of load_cytoframe_from_cytoset is a single cytoframe we can't automatically read in all available sets. This parameter allows the user to choose one of the subsets for import. Its value should be an integer in the range of available data sets. This argument is ignored if there is only a single data segment in the FCS file.
emptyValue	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.
num_threads	Integer allowing for parallelization of the parsing operation by specifiying a number of threads
ignore.text.offset	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.
text.only	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 read.AnnotatedDataFrame, see details

Details

The function 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 cytoframe.

For specifications of FCS 3.0 see http://www.isac-net.org and the file ../doc/fcs3.html in the doc directory of the package.

The 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).

Value

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.

See Also

Other cytoframe/cytoset IO functions: cf_get_uri(), cf_write_disk(), cf_write_h5(), cf_write_tile(), cs_get_uri(), load_cytoframe(), load_cytoset_from_fcs()

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.