VDJ utility for T/F column for clonal expansion

Source: R/VGM_expanded_clones.R

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.

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


#Add info to whole VGM object
VGM <- VGM_expanded_clones(
VGM = Platypus::small_vgm, add.to.VDJ = TRUE, add.to.GEX = TRUE,
expansion.threshold = 1)
#> Added new columns to VDJ: expanded_clonotype_frequency
#> Added new columns to GEX: expanded_clonotype_frequency