Inference with different databases of miRNA‐target interactions

The miRTalkDB contains the miRNA-target interactions obtained from the two databases, miRTarBase and TarBase. Given the large size for the TarBase, the default selection in miRTalk is the miRTarBase with the parameter database = "miRTarBase" in the function find_miRNA. We allow users to select the different database with the parameter database in the function find_miRNA. Step-by-step procedures are shown below:

[1] load the example data

> load(paste0(system.file(package = 'miRTalk'), "/extdata/example.rda"))

> dim(sc_data)
[1] 22898   515

> table(sc_celltype)
sc_celltype
  Bcell Myeloid Stromal   Tcell   Tumor 
     83      38      23      54     317 

[2] create miRTalk object using single-cell transcriptomics data

> obj <- create_miRTalk(sc_data = sc_data,
                        sc_celltype = sc_celltype,
                        species = "Human",
                        condition = rep("condition",length(sc_celltype)),
                        evbiog = evbiog,
                        risc = risc,
                        ritac = ritac)
Warning: The following features are not present in the object: AGO2, not searching for symbol synonyms

[3] Find highly variable target genes with DEGs and HVGs with find_hvtg

> obj <- find_hvtg(object = obj)

[4] Find expressed miRNAs among all cells and generate background distribution for permutation test with find_miRNA. Set the parameter database

> table(mir2tar[mir2tar$source == "TarBase-v9.0",]$species) # number of miRNA-target interactions in TarBase
  Human   Mouse     Rat 
4601489 1065375    1083

> table(mir2tar[mir2tar$source != "TarBase-v9.0",]$species) # numberf of miRNA-target interactions in miRTarBase
 Human  Mouse    Rat 
495217  48480    632

• select miRTarBase

> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    database = "miRTarBase")

• select TarBase

> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    database = "TarBase")

• select both

> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    database = c("miRTarBase", "TarBase"))

[5] Infer cell-cell communication mediated by EV-derived miRNAs from senders to receivers

> obj <- find_miRTalk(obj, if_doParallel = F)
[condition] 
[++++++++++++++++++++++++++++++] Finished:100% time:00:04:57