Description Usage Arguments Value Examples
Reads and combines data from many FCS files for use with Citrus.
1 2 3 4 |
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 |
... |
Other undocumented parameters. |
An object of type citrus.combinedFCSSet
.
data |
Combined FCS measurements from files listed in fileList, with paraemters |
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 |
1 2 3 4 5 6 7 8 9 | 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)
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