testGatingMLCompliance: Function to perform all the Gating-ML compliance tests

In jspidlen/flowUtils: Utilities for flow cytometry

Description

This function performs the Gating-ML compliance tests. Either Gating-ML 1.5 or Gating-ML 2.0 compatibility may be checked. The Gating-ML XML files, FCS data files and the expected results provided by the gatingMLData are utilized in performing the compliance tests. The results obtained are compared with the expected results and an HTML summary report is generated.

Usage

  testGatingMLCompliance(file = "GatingMLComplianceReport", version = 2.0)

Arguments

file	Name of the file in which the generated Gating-ML compliance report is to be saved. The .html extension will be added.
version	The Gating-ML version that is supposed to be checked. Currently, versions 1.5 and 2.0 are supported.

Details

The testGatingMLCompliance function depends on the gatingMLData data package for performing the compliance tests.

Author(s)

Spidlen J., Gopalakrishnan N.

References

Spidlen J, ISAC DSTF, Brinkman RR. 2014.
Gating-ML 2.0. International Society for Advancement of Cytometry (ISAC) standard for representing gating descriptions in flow cytometry.
http://flowcyt.sf.net/gating/20141009.pdf
http://flowcyt.sf.net/gating/20141009.full.zip

Spidlen J, Leif RC, Moore W, Roederer M; International Society for the Advancement of Cytometry Data Standards Task Force, Brinkman RR.
Gating-ML: XML-based gating descriptions in flow cytometry.
Cytometry A. 2008 Dec; 73A(12):1151–7. doi: 10.1002/cyto.a.20637.

Spidlen J, ISAC DSTF, Brinkman RR. 2008.
Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry version 1.5.
http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.pdf
http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.full.zip
http://flowcyt.sf.net/gating/Gating-ML.v1.5.081030.Compliance-tests.081030.zip

Examples

## Not run: 
################################################################
### Performs Gating-ML 1.5 compliance tests and                #
### writes the results to Gating-ML_1.5_Compliance_Report.html #
################################################################
testGatingMLCompliance("Gating-ML_1.5_Compliance_Report", version = 1.5)

################################################################
### Performs Gating-ML 2.0 compliance tests and                #
### writes the results to Gating-ML_2.0_Compliance_Report.html #
################################################################
testGatingMLCompliance("Gating-ML_2.0_Compliance_Report", version = 2.0)

## End(Not run)

jspidlen/flowUtils documentation built on Nov. 4, 2019, 3:25 p.m.