ReadFCSSet: Read a set of FCS files for analysis

Description Usage Arguments Value Examples

Description

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

Usage

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ReadFCSSet(dataDirectory, fileList, fileSampleSize = 1000,
  transformColumns = NULL, transformCofactor = 5,
  scaleColumns = NULL, useChannelDescriptions = F,
  readParameters = NULL, verbose = TRUE, ...)

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.

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.

Examples

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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)

Mamie/mwang documentation built on May 14, 2019, 7:15 p.m.