read.flowSet {flowCore} | R Documentation |
Read one or several FCS files: Data File Standard for Flow Cytometry
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, ...)
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
phenoData slot. |
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. |
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)
.
An object of class flowSet-class{flowSet}
.
F. Hahne, N.Le Meur, B. Ellis
fcs.loc <- system.file("extdata",package="flowCore") file.location <- paste(fcs.loc, dir(fcs.loc), sep="/") samp <- read.flowSet(file.location[1:3])