only 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.

only 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.

VDJ_GEX_integrate(GEX.object, clonotype.list, VDJ.per.clone, clonotype.level)

Arguments

GEX.object

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

clonotype.list

Output from either VDJ_analyze or VDJ_clonotype functions. This list should correspond to a single GEX.list object, in which each list element in clonotype.list is found in the GEX.object. Furthermore, these repertoires should be found in the automate_GEX library.

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.

clonotype.level

Logical specifying whether the integration should occur on the cellular level (VDJ_per_clone) or on the clonotype level (e.g. output from VDJ_analyze or VDJ_clonotype). TRUE specifies that the clonotype level will be selected - e.g. the clonotype.list object will now contain information from the GEX object regarding clonal membership.

Value

Returns a nested list containing information corresponding to either the clonal level or the sequence level, depending on the input argument "clonotype.level". This function essentially will update the output of the analyze_VDJ or the VDJ_per_clone functions.

Examples

if (FALSE) {
testing_integrate <- VDJ_GEX_integrate(GEX.object = automate.gex.output[[1]]
,clonotype.list =  VDJ.analyze.output
,VDJ.per.clone = VDJ.per.clone.output,clonotype.level = TRUE)
}