VGM_expanded_clones: VDJ utility for T/F column for clonal expansion

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

VDJ utility for T/F column for clonal expansion

Description

Adds discrete columns containing TRUE / FALSE on whether a given cell is part of a expanded or not-expanded clonotype. Threshold frequency can be set.

Usage

VGM_expanded_clones(VGM, add.to.VDJ, add.to.GEX, expansion.threshold)

Arguments

VGM	Output object from the VDJ_GEX_matrix function (VDJ_GEX_matrix.output)
add.to.VDJ	Boolean. Whether to add expanded columns to VDJ matrix. Defaults to TRUE
add.to.GEX	Boolean. Whether to add expanded columns to GEX matrix. Defaults to TRUE
expansion.threshold	Integer. Defaults to 1. Cells in clonotypes above this threshold will be marked as expanded = TRUE.

Value

An output object from the VDJ_GEX_matrix function with added columns containing TRUE / FALSE values based on clonotype frequency.

Examples

VGM <- VGM_expanded_clones(
VGM = Platypus::small_vgm, add.to.VDJ = TRUE, add.to.GEX = TRUE,
expansion.threshold = 1)

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.