Platypus V2 dataframe utility — VDJ_reclonotype_list

Only Platypus v2 Organizes the top N genes that define each Seurat cluster and converts them into a single dataframe. This can be useful for obtaining insight into cluster-specific phenotypes.

VDJ_reclonotype_list_arrange(
  VDJ_clonotype.output,
  VDJ_analyze.output,
  Platypus_list.object
)

Arguments

VDJ_clonotype.output: The output object from the VDJ_clonotype function. The column of the merged nucleotide clonotype IDs will be used to rearrange the new object.
VDJ_analyze.output: The output from the initial VDJ_analyze, containing clonotype information based on nucleotide sequence.
Platypus_list.object: The new list object from one of Platypus functions (for example, clonal lineages, VDJ_per_clne, etc) that should be merged based on the VDJ_clonotype output structure. nested list structure, where outer list corresponds to repertoire and the inner list corresponds to clones (on the nucleotide level).

Value

Returns a dataframe in which the top N genes defining each cluster based on differential expression are selected.

Examples

if (FALSE) {
checking_vdj_reclono <- VDJ_reclonotype_list_arrange(
VDJ_clonotype.output = repertoire_reclonotype
,VDJ_analyze.output = repertoire_list
,Platypus_list.object = repertoire_vdj_per_clone)
}