Up: Component summary Component

Summarise

Summarises values for different rows of a file (i.e. reference) according to the clustered and possibly filtered result of the file (i.e. clusterFiles). A column should be assigned to row IDs of the reference file. This is to keep the track of possible filterings in the clusterFiles.

Version 1.0
Bundle flowand
Categories FlowCytometry
Authors Ali Oghabian (ali.oghabian@helsinki.fi)
Requires R
Source files component.xml Summarise.r
Usage Example with default values

Inputs

Name Type Mandatory Description
clusterFiles CSVList Mandatory Filtered files directory. A column should be assigned to the row id numbers according to the original Pre-filtered data (i.e. reference parameter). An additional column should also be aassigned to the cluster numbers of the rows (i.e. Event IDs in flow cytometry analysis). clusterFiles should have the same names as the reference files.
reference CSVList Mandatory The reference CSV files. The Compensated data-table is recomended in flow cytometry analysis. A column should be assigned to the row id numbers (e.g. Event IDs in flow cytometry analysis). If the summaries are required to be calculated for the clustered files, the same link as the clusterFiles could be assigned to reference.

Outputs

Name Type Description
summaries CSVList csv files including the summary tables i.e. summary values for each cluster of the files. each row represents a cluster number which could be accessed through "cluster" column and other clusters include the summary calculations of the related columns in the rows grouped in similar clusters.

Parameters

Name Type Default Description
clusterCol string "cluster" The name of the column in the clusterFiles which represents the cluster number of the rows.
culsterIDCol string "Event" The name of the column in the clusterFiles which represents the Row IDs, row names or the Event numbers of the cells in flow cytometry analysis.
referenceIDCol string "Event" The name of the column in the reference files which represents the Row IDs, row names or the Event numbers of the cells in the flow cytometry analysis.
summaryType string "mean" The summary type of interest. Three types of mean, median, and var are available.

Test cases

Test case Parameters IN
clusterFiles
IN
reference
OUT
summaries
case1 properties clusterFiles reference summaries

summaryType=mean


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