load_cytoset_from_fcs {flowWorkspace} | R Documentation

## Read one or several FCS files in to a cytoset

### Description

Similar to `read.flowSet`, this takes a list of FCS filenames and returns a `cytoset`.

### Usage

    load_cytoset_from_fcs(
      files = NULL,
      path = ".",
      pattern = NULL,
      phenoData = NULL,
      descriptions,
      name.keyword,
      transformation = "linearize",
      which.lines = NULL,
      alter.names = FALSE,
      column.pattern = NULL,
      invert.pattern = FALSE,
      decades = 0,
      is_h5 = NULL,
      h5_dir = NULL,
      backend = get_default_backend(),
      backend_dir = tempdir(),
      min.limit = NULL,
      truncate_max_range = TRUE,
      dataset = NULL,
      emptyValue = TRUE,
      num_threads = 1,
      ignore.text.offset = FALSE,
      sep = "\t",
      as.is = TRUE,
      name,
      file_col_name = NULL,
      ...
    )

### Arguments

`files` | Optional character vector with filenames.
`path` | Directory where to look for the files.
`pattern` | This argument is passed on to `dir`, see details.
`phenoData` | An object of class `AnnotatedDataFrame`, `character` or a list of values to be extracted from the `cytoframe` object, see details.
`descriptions` | Character vector to annotate the object of class `cytoset`.
`name.keyword` | An optional character vector that specifies which FCS keyword to use as the sample names. If this is not set, the GUID of the FCS file is used for sampleNames, and if that is not present (or not unique), then the file names are used.
`transformation` | see `load_cytoframe_from_fcs` for details.
`which.lines` | see `load_cytoframe_from_fcs` for details.
`alter.names` | see `load_cytoframe_from_fcs` for details.
`column.pattern` | see `load_cytoframe_from_fcs` for details.
`invert.pattern` | see `load_cytoframe_from_fcs` for details.
`decades` | see `load_cytoframe_from_fcs` for details.
`is_h5` | logical indicating whether the data should be stored in h5 format
`h5_dir` | String specifying a name for the h5 directory for the h5 files if `is_h5` is TRUE
`min.limit` | see `load_cytoframe_from_fcs` for details.
`truncate_max_range` | see `load_cytoframe_from_fcs` for details.
`dataset` | see `load_cytoframe_from_fcs` for details.
`emptyValue` | see `load_cytoframe_from_fcs` for details.
`num_threads` | Integer allowing for parallelization of the parsing operation by specifiying a number of threads
`ignore.text.offset` | see `load_cytoframe_from_fcs` for details.
`sep` | Separator character that gets passed on to `read.AnnotatedDataFrame`.
`as.is` | logical that gets passed on to `read.AnnotatedDataFrame`. This controls the automatic coercion of characters to factors in the `phenoData`.
`name` | An optional character scalar used as name of the object.
`file_col_name` | optionally specify the column name that stores the fcs filename when phenoData is supplied `read.AnnotatedDataFrame`, see details.
`...` | Further arguments that get passed on to

### Details

There are four different ways to specify the file from which data is to be imported:

First, if the argument `phenoData` is present and is of class `AnnotatedDataFrame`, then the file names are obtained from its sample names (i.e. row names of the underlying data.frame). Also column `name` will be generated based on sample names if it is not there. This column is mainly used by visualization methods in flowViz. Alternatively, the argument `phenoData` can be of class `character`, in which case this function tries to read a `AnnotatedDataFrame` object from the file with that name by calling `read.AnnotatedDataFrame(file.path(path,phenoData),...{})`.

In some cases the file names are not a reasonable selection criterion and the user might want to import files based on some keywords within the file. One or several keyword value pairs can be given as the phenoData argument in form of a named list.

Third, if the argument `phenoData` is not present and the argument `files` is not `NULL`, then `files` is expected to be a character vector with the file names.

Fourth, if neither the argument `phenoData` is present nor `files` is not `NULL`, then the file names are obtained by calling `dir(path, pattern)`.

### Value

An object of class `cytoset`.

### See Also

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

[Package flowWorkspace version 4.2.0 Index]