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,alter.names=FALSE, transformation =
  "linearize", which.lines=NULL, debug = FALSE, column.pattern = NULL,
  decades=0,sep="\t", as.is=TRUE, name, ncdf=FALSE, ...)

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 flowFrame object, see details.
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. 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.
alter.names see read.FCS for details.
transformation see read.FCS for details.
which.lines see read.FCS for details.
debug see read.FCS for details.
column.pattern see read.FCS for details.
decades see read.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 phenoDataslot.
name An optional character scalar used as name of the object.
ncdf Instead of reading all data into memory, this switches to file-based data storage. See read.FCS for details.
... Further arguments that get passed on to read.AnnotatedDataFrame, see details.

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. 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(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 flowSet-class{flowSet}.

Author(s)

F. Hahne, N.Le Meur, B. Ellis

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 1.10.0 Index]