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MetaClustering

Meta-Clustering for defining isomorphisms on cells across clusters.

Version 0.1
Bundle flowand
Categories FlowCytometry
Authors Javier Nunez Fontarnau (Javier.Nunez-Fontarnau@Helsinki.FI), Ali Oghabian (ali.oghabian@helsinki.fi)
Requires R ; flowCore (R-bioconductor) ; cluster (R-package) ; lpSolve (R-package)
Source files component.xml MetaClustering.r
Usage Example with default values

Inputs

Name Type Mandatory Description
optimalClustering CSVList Mandatory Full pathname to optimal gating files directory.

Outputs

Name Type Description
metaClusters CSVList The aligned cluster files
metaAssign CSVList The assignment of the input clusters to the Metaclusters

Parameters

Name Type Default Description
IPDelta float 0.05 The parameter delat for the Integer Programming (i.e. the IP function)
clusterCol string "cluster" The name of the column which represents the cluster number of the rows.
kMaxPam int 0 Maximum number of pams clusters to be tested for the Metaclustering. By default the Maximum of available (i.e. real) mixture model clusters would be assumed.
kMinPam int 0 Minimum number of pams clusters to be tested for the Metaclustering. By default the Minimum of available (i.e. real) mixture model clusters would be assumed.
medianFactor float 0.2 A value between 0 and 1, describing the fraction of the metaclusters to be considered for median analysis.
metaClusterChannels string "NA" Channels to consider for the metaclustering process. Cluster column could be included. The parameter could be set as "1, 2, 3, 4, 5, 6" or "FSC.A, SSC, ERK1, STAT1, CD4, cluster"
randomSeed int 1984 The seed value for semi-random processes

Test cases

Test case Parameters IN
optimalClustering
OUT
metaClusters
OUT
metaAssign
case1 properties optimalClustering metaClusters metaAssign

kMinPam =4,
kMaxPam =6,
metaClusterChannels=2, 3, 4, 5, 6, 7, 8, 9, 10, 11


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