Platypus V2 GEX and VDJ integration for clonotypes

Source: R/GEX_clonotype.R

Platypus V2: Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object and the index of the cell in the Seurat RNA-seq object.

GEX_clonotype(GEX.object, VDJ.per.clone)

Arguments

GEX.object

A single seurat object from automate_GEX function. This will likely be supplied as automate_GEX.output[[1]].

VDJ.per.clone

Output from the VDJ_per_clone function. Each element in the list should be found in the output from the automate_GEX function.

Value

Returns a dataframe containing repertoire information, such as isotype, CDR sequences, mean number of UMIs. This output can be supplied to furhter packages VDJ_extract_sequences and VDJ_GEX_integrate

Examples

if (FALSE) {
GEX_clonotype(GEX.object=automate.GEX.output[[1]], VDJ.per.clone=vdj.per.clone.output)
}