read.flowSet {flowCore}R Documentation

Read a set of FCS files

Description

Read one or several FCS files: Data File Standard for Flow Cytometry

Usage

   read.flowSet(files=NULL, path=".",pattern=NULL,phenoData,descriptions,name.keyword,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 An object of class phenoData, character or a list of values to be extracted from the flowFrame object.
descriptions Character vector to annotate the object of class flowSet-class{flowSet}.
name.keyword An optional character vector that specifies which FCS keyword to use as the sample names.
sep Separator character that gets passed on to read.phenoData.
... Further arguments that get passed on to read.FCS, see details.

Details

There are three different ways to specify the file names:

First, if the argument phenoData is present and is of class phenoData, 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 phenoData object from the file with that name by calling read.phenoData(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 flowSet-class{flowSet}.

Author(s)

F. Hahne, N.Le Meur

Examples


fcs.loc <- system.file("extdata",package="flowCore")
file.location <- paste(fcs.loc, dir(fcs.loc), sep="/")

samp <- read.flowSet(file.location[1:3])


[Package flowCore version 1.0.2 Index]