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

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.

Value

cytoSet.

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).

Examples

Run this code

## Please see man page for cytoSet-class