View source: R/VDJ_GEX_integrate.R
VDJ_GEX_integrate | R Documentation |
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)
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. |
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.
## Not run: 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) ## End(Not run)
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