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FlowClustModeling

Modeling FACS data using flowClust library

Version 0.1
Bundle flowand
Categories FlowCytometry
Authors Anna-Maria Lahesmaa-Korpinen (anna-maria.lahesmaa@helsinki.fi)
Requires R ; flowCore (R-bioconductor) ; flowClust (R-bioconductor) ; geneplotter (R-bioconductor)
Source files component.xml FlowClustModeling.r
Usage Example with default values

Inputs

Name Type Mandatory Description
fcsDir CSVList Mandatory Directory for FCS files in CSV format.

Outputs

Name Type Description
clusters CSVList Clustered data files, with last column as cluster number.
report Latex Visualization of compensation results. Contains jpeg for each original file.

Parameters

Name Type Default Description
channelsToCluster string (no default) A comma-separated list of channel/antibody numbers, to be clustered (e.g., "SSC.A,CD4,CD3,CD45").
clusterIDColName string "cluster" The name of the column in the clusters output which contains the cluster IDs of the rows.
height float 250 Height of plot per channel in px.
keepOriginalChannelNames boolean false If true, original channel names are kept. Usually these are the antibody names. If false, channel names are replaced with the descriptions of the channels, if they exist. These are the names of the proteins targeted by the antibodies.
level float 0.9 A numeric value between 0 and 1 specifying the threshold quantile level used to call a point an outlier. The default is 0.9, meaning that any point outside the 90% quantile region will be called an outlier.
maxClusters int 2 An integer indicating the maximum number of clusters.
minClusters int 1 An integer indicating the minimum number of clusters.
numIterations int 100 The maximum number of EM iterations.
pagebreak boolean false Tells if the result document should start with a page break.
width float 250 Width of plot per channel in px.

Test cases

Test case Parameters IN
fcsDir
OUT
clusters
OUT
report
case1 properties fcsDir clusters report

channelsToCluster=FSC.H,SSC.H


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