citrus.readFCSSet: Read a set of FCS files for analysis

In nolanlab/citrus: Citrus: Identification of stratifying subpopulations in Flow Cytometry Data.

Read a set of FCS files for analysis

Description

Reads and combines data from many FCS files for use with Citrus.

Usage

citrus.readFCSSet(dataDirectory, fileList, fileSampleSize = 1000,
  transformColumns = NULL, transformCofactor = 5, scaleColumns = NULL,
  useChannelDescriptions = F, readParameters = NULL, ...)

print.citrus.combinedFCSSet(citrus.combinedFCSSet)

Arguments

dataDirectory	Full or relative path to directory containin FCS files.
fileList	Data frame containing names of files to be read. Each entry should be a file name. FCS files from the same experimental condition should be listed in the same column with the column name indicating the experimental condition. FCS files from the same sample measured in multiple experimental conditions should be listed in the same row. See examples.
fileSampleSize	Number of cells to be selected from each FCS file. If this number is larger than the number of events in a given FCS file, all cells from that file are selected.
transformColumns	Vector of parameter names or indicies whose values should transformed prior to analysis.
scaleColumns	Vector of parameter names or indicies whose values should be scaled prior to analysis.
useChannelDescriptions	Should channel descriptive names be used to name data instead of channel names?
readParameters	Vector of parameter names (or descriptions if useChannelDescriptions='T') to be read from each FCS file. Can be used to specify common parameters among FCS files that contain different measured parameters.
...	Other undocumented parameters.
Cofactor	for arcsin-hyperbolic transform.

Value

An object of type citrus.combinedFCSSet.

data	Combined FCS measurements from files listed in fileList, with paraemters fileEventNumber and fileId added. The former reports the event number in the original source file and the latter records the file from which the event was sampled.
fileIds	A matrix recording the assigned fileIds for each file in the fileList argument.
fileNames	The corresponding file names for each file, indexed by fileId.
fileChannelNames	Names of parameters in each read file.
fileReagentNames	Description of parameters in each read file.
transformColumns	List of columns that were transformed when read, if supplied.
transformCofactor	Cofactor used for arcsinh transformation, if applicable.

Author(s)

Robert Bruggner

Examples

dataDirectory = file.path(system.file(package = "citrus"),"extdata","example1")

# Create list of files to be analyzed - one condition.
fileList = data.frame("unstim"=list.files(dataDirectory,pattern=".fcs"))
citrus.combinedFCSSet = citrus.readFCSSet(dataDirectory,fileList)

# Create list of files to be analyzed - two conditions.
fileList = data.frame(unstim=list.files(dataDirectory,pattern="unstim"),stim1=list.files(dataDirectory,pattern="stim1"))
citrus.combinedFCSSet = citrus.readFCSSet(dataDirectory,fileList)

nolanlab/citrus documentation built on April 19, 2024, 6:49 p.m.