simplifyGateNames {flowFlowJo} | R Documentation

## Standardize flow cytometry gate names

### 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 + ")

[Package flowFlowJo version 1.2.0 Index]