simplifyGateNames {flowFlowJo} | R Documentation |
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".
simplifyGateNames(x, ...)
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. |
This function returns either a text string or flowCore style filter object.
John Gosink
simplifyGateNames(c("LymphoCytes", "lymphocytes", "mOnOcYtEs")); simplifyGateNames(c("Lymphocytes:CD8+"), removeParentalNames=TRUE); simplifyGateNames("CD34 positive cells ") simplifyGateNames("CD34 + ")