Use human data for the inference of mouse and rat data

Considering that limited miRNA-target interactions for mouse and rat in relative to human, we add a parameter if_use_human_data in the function find_miRNA, namely whether to use homologous human data in mir_info and mir2tar for mouse or rat scRNA-seq data. For human scRNA-seq data, no need to do it. For mouse or rat data, you can set it TRUE. 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 if_use_human_data as TRUE to use human data about miRNA-target interactions. To combine the human data and raw mouse/rat data, set the parameter if_combine as TRUE. gene2gene must be provided when if_use_human_data = TRUE

> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    if_use_human_data = TRUE,
                    gene2gene = gene2gene)
# or 
> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    if_use_human_data = TRUE,
                    if_combine = TRUE,
                    gene2gene = gene2gene)

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

> obj <- find_miRTalk(obj, if_doParallel = F)