VDJ_expand_aberrants: Expand the aberrant cells in a VDJ dataframe by converting...

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

Expand the aberrant cells in a VDJ dataframe by converting them into additional rows

Description

Expand the aberrant cells in a VDJ dataframe by converting them into additional rows. Aberrant cells consist of cells with more than 1 VDJ or VJ chain.

Usage

VDJ_expand_aberrants(
  VDJ,
  chain.to.expand,
  add.barcode.prefix,
  additional.VDJ.features,
  additional.VJ.features,
  add.CDR3aa,
  add.expanded.number,
  recalculate.clonotype.frequency
)

Arguments

VDJ	VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.
chain.to.expand	string, 'VDJ' to expand VDJ aberrants, 'VJ' to expand VJ aberrants, 'VDJ.VJ' for both.
add.barcode.prefix	boolean - if T, a new barcode will be added for each expanded aberrant.
additional.VDJ.features	vector of strings - VDJ_expand_aberrants will only expand across the sequence columns of VDJ. If you have additional columns with aberrant cell features (e.g., both 'yes' and 'no' binders for a single sequence), where the aberrants are VDJ-specific, include them here.
additional.VJ.features	vector of strings - VDJ_expand_aberrants will only expand across the sequence columns of VDJ. If you have additional columns with aberrant cell features (e.g., both 'yes' and 'no' binders for a single sequence), where the aberrants are VJ-specific, include them here.
add.CDR3aa	boolean - if T, will create a new column 'CDR3aa' with pasted VDJ_cdr3s_aa and VJ_cdr3s_aa.
add.expanded.number	boolean - if T, will add the number of new cells resulting from an aberrant one.
recalculate.clonotype.frequency	boolean - if T, will recalculate the clonotype frequencies for the resulting, expanded VDJ.

Value

Returns a VDJ format dataframe in which cells with more than one VDJ or VJ chain are split into multiple rows each containing only one VDJ VJ chain combination.

Examples

VDJ_expand_aberrants(VDJ = small_vgm[[1]],
chain.to.expand='VDJ.VJ',
add.barcode.prefix=TRUE, recalculate.clonotype.frequency=FALSE)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.