readCytoSet {prada} | R Documentation |
Create a cytoSet object from one or more FCS 3.0 files
readCytoSet(files=NULL, path=".", pattern=NULL, phenoData, 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 |
Either an object of class phenoData or
character . |
sep |
Separator character that gets passed on to
read.phenoData . |
... |
Further arguments that get passed on to
read.phenoData , 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 cytoSet
.
Wolfgang Huber http://www.ebi.ac.uk/huber
## Please see man page for cytoSet-class