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ClusterFiltering

Filters columns and/or rows from by clusters using flexible criteria. Possible to filter clusters out by minimum number of events/cluster or by relative median/mean value of cluster centers.

Version 1.0
Bundle flowand
Categories FlowCytometry
Authors Erkka Valo (erkka.valo@helsinki.fI), Ping Chen (ping.chen@helsinki.fi), Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi)
Requires R
Source files component.xml ClusterFiltering.r
Usage Example with default values

Inputs

Name Type Mandatory Description
fcsDir CSVList Optional A Directory containing CSV files that represent samples measured in FACS experiment. Rows represent cells and columns measured variables. Each file should contain one column representing clusters.
in Array<CSV> Optional An array of CSV files for samples from a FACS experiment.

Outputs

Name Type Description
filtered CSVList A Folder containing the filtered FCS files.
out Array<CSV> Array of filtered CSV files.

Parameters

Name Type Default Description
clusterColumn string "" The name of the column which contains cluster indexes.
combineMethod string "median" The method used for combining intensities for each cluster. It can be 'median' or 'mean'. Note: filtering is done based on the combined data for each cluster.
filterColumn string "" A comma-separated channel IDs based on which the filtering is done. If filtering is based on all channels, set it to '*'.
filterDiff float 0.0 Difference of cluster center to median of all cluster centers.
minCellNumber int 10 The minimum number of cells in a cluster. If a cluster contains cells less than this threshold, all the cells in the cluster will be removed.

Test cases

Test case Parameters IN
fcsDir
IN
in
OUT
filtered
OUT
out
case1 properties fcsDir (missing) filtered (missing)

minCellNumber=2,
filterColumn=FITC-A,PE-A,
clusterColumn=Cluster

case2 properties fcsDir (missing) filtered (missing)

minCellNumber=2,
filterColumn=FSC.A,SSC.A,CD45,
clusterColumn=cluster

case3_mixedarray properties fcsDir in filtered (missing)

minCellNumber=2,
filterColumn=FITC-A,PE-A,
clusterColumn=Cluster


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