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SamSpectral

SamSPECTRAL clustering of flow cytometry data as described by Zare et al (2010).

More info in Bioconductor documentation.

Version 1.1
Bundle flowand
Categories FlowCytometry
Authors Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi)
Requires R ; SamSPECTRAL (R-bioconductor) ; Rmpi (R-package)
Source files component.xml SamSpectral.r
Usage Example with default values

Inputs

Name Type Mandatory Description
list CSVList Optional Location of the csv files to be clustered e.g. Preprocessed files in flow cytometry analysis .
in Array<CSV> Optional An Array of CSV files to be clustered e.g. Preprocessed files in flow cytometry analysis.

Outputs

Name Type Description
clusters CSVList csv files including the input data and one additional column presenting the clustering results. The numbers added to the input filenames represent the number of clusters found.
out Array<CSV> csv files including the input data and one additional column presenting the clustering results. The numbers added to the input filenames represent the number of clusters found.

Parameters

Name Type Default Description
channelsToCluster string (no default) A comma-separated list of column names or column numbers (e.g. channel names/ numbers in flow cytometry analysis), to be clustered. As for instance the value could be set as "1, 2, 3, 4, 5" or "FSC.A, SSC, ERK1, STAT1, CD4" .
clusterIDColName string "cluster" The name of the column in the clusters output which contains the cluster IDs of the rows.
separationFactor float 0.5 This threshold controls to what extend clusters should be combined or kept separate. Normally, an appropriate value will fall in range 0.3-2.
sigma int 100 A scaling parameter typically between 10...1000. It determines the "resolution" in the spectral clustering stage. By increasing it, more spectral clusters are identified. This can be useful when "small" population are aimed.

Test cases

Test case Parameters IN
list
IN
in
OUT
clusters
OUT
out
case1 properties list (missing) clusters (missing)

channelsToCluster=FSC-H,SSC-H,
clusterIDColName=id

case2 properties list in clusters (missing)

channelsToCluster=FSC-H,SSC-H,
clusterIDColName=id


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