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,sep="\t",...)
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. |
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)
.
An object of class flowSet-class{flowSet}
.
F. Hahne, N.Le Meur
fcs.loc <- system.file("extdata",package="flowCore") file.location <- paste(fcs.loc, dir(fcs.loc), sep="/") samp <- read.flowSet(file.location[1:3])