readCytoSet: Create a cytoSet object from one or more FCS 3.0 files

In prada: Data analysis for cell-based functional assays

Description

Create a cytoSet object from one or more FCS 3.0 files

Usage

  readCytoSet(files=NULL, path=".", pattern=NULL, phenoData, sep="\t", ...)

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	Either an object of class phenoData or character.
sep	Separator character that gets passed on to read.AnnotatedDataFrame.
...	Further arguments that get passed on to read.AnnotatedDataFrame, see details.

Details

There are three different ways to specify the file names:

First, if the argument phenoData is present and is of class AnnotatedDataFrame, then it is obtained from its column name. The column is mandatory, and an error will be generated if it is not there. 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 with arguments file.path(path, phenoData), ....

Second, 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.

Third, 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.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

See Also

readFCSdata

Examples

## Please see man page for cytoSet-class

prada documentation built on April 28, 2020, 7:52 p.m.