simplifyGateNames: Standardize flow cytometry gate names

In flowFlowJo: Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.

Description

This function helps to standardize typical flow cytometry cell population names. This is useful when trying to combine the results from a large number of flow runs wherein the cytometrist may have used slightly different nomenclature to describe the same set of cells. For example, "Lymphocytes" vs. "lymphoctes".

Usage

 
simplifyGateNames(x, ...) 

Arguments

x

Logical. Default=FALSE. A flowCore style filter, or a text string with a gate (filter) name

...

Additional arguments: upperCaseGates Logical. Default=FALSE. If TRUE, convert the gate names to all upper case stripFileName Logical. Default=TRUE. It is currently the convention that the flowFlowJo code prepends the name of the referenced FCS file within the gate name, followed by a colon, then the rest of the gate information. This setting looks for ".*\.fcs:" and strips it out of the gate name removeParentalNames Logical. Default=TRUE. The current getFlowJoGates method concatenates a gate's name with the name of all of it's parents.

Value

This function returns either a text string or flowCore style filter object.

Author(s)

John Gosink

Examples

 
simplifyGateNames(c("LymphoCytes", "lymphocytes", "mOnOcYtEs"));
simplifyGateNames(c("Lymphocytes:CD8+"), removeParentalNames=TRUE); 
simplifyGateNames("CD34 positive cells ") 
simplifyGateNames("CD34 + ") 

flowFlowJo documentation built on Sept. 12, 2016, 6:14 a.m.