TreeMetaRenaming: Automatic naming of metaclustesters according to specific...

In gautierstoll/CytoSOM: Easy use of FlowSOM

Description

A name based of markers level is added to the metcluster names (of number, in that case, the numbers are kept in the object as $metaClNumber)

Usage

TreeMetaRenaming(TreeMetaCl, Markers, Levels, CutOff = NULL, Short = FALSE)

Arguments

TreeMetaCl	Object generated by the function BuildFSOMTree
Markers	vector of markers used for naming
Levels	number of level for naming: 2 -> -/+ (1/2-4 quartiles), 3-> -/low/high (1/2-3/4 quartiles), 4-> -/low/int/high (1/2/3/4 quartiles)
CutOff	matrix for optional cut off values for naming, with markers in row.names, each column for separating levels. If a marker is not in row.names, quartiles are used
Short	is true, low is not represented with Levels=3, int is not represented if Levels = 4

Value

BuildFSOMTree object with the metaclusters renamed with the choosen name type, keeping the metacluster numbers ($metaClNumber)

Examples

CytoTreeNewNames <- TreeMetaRenaming(TreeMetaCl=CytoTree,Markers=c("CD4","CD8","FoxP3"),Levels=4)

gautierstoll/CytoSOM documentation built on May 16, 2020, 10:36 a.m.