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FlowMeans

Clusters rows in CSV files. The component is a wrapper for the R-package flowMeans. Clustering is based on k-means clustering but spherichal clusters are merged to find non-spherichal clusters.

Version 1.0
Bundle flowand
Categories FlowCytometry
Authors Erkka Valo (erkka.valo@helsinki.fi)
Requires flowMeans (R-package)
Source files component.xml FlowMeans.r
Usage Example with default values

Inputs

Name Type Mandatory Description
inList CSVList Optional CSV files to cluster.
in Array<CSV> Optional CSV files to cluster.

Outputs

Name Type Description
clustersList CSVList Clustered CSV files.
clusters Array<CSV> Clustered CSV files.
report Latex Report of the clustering.

Parameters

Name Type Default Description
channelsToCluster string "*" The columns used to cluster the data in a comma-separated list. Default value "*" uses all columns. If all the columns are not present in a input csv file, the clustering is done with the subset of columns that are present.
clusterIDColName string "cluster" The name of the column in the clusters output which contains the cluster IDs of the rows.
iterMax int 50 The maximum number of iterations allowed.
mahalanobis boolean true If TRUE (default) mahalanobis distance will be used. Otherwised, euclidean distance will be used.
maxN int -1 Maximum number of clusters. If set to a negative value (default) the value will be estimated automatically from the data.
nStart int 10 The number of random sets used for initialization.
numC int -1 Number of clusters. If set to a negative value (default), the value will be estimated automatically.
standardize boolean true If TRUE, the data will be transformed to the [0,1] interval for clustering. The transformed values are not put into the output files.

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