Ligand-Receptor Database

List of ligand-receptor pairs consolidated from iTalk, SCSR, Phantom5, NATMI and Moffat Lab (in house).

{
data(LR.db)


# To update list:

# import data
load("C:/Users/Owner/Dropbox/PDF Projects - JM/Data/scRNA-seq/01_sci-RNA-seq3_Hong_Kevin_Jason/NM_HH/Data/Gene_Sets/LR.db_Magali_301120.RData")

# parse databases
list.source <- strsplit(LR.db$Which_db, " ") # LR.db$Which_db
names(list.source) <- LR.db$Pair

all.db <- unique(unlist(list.source))
db.list <- list()
for (i in 1:length(all.db)){
  db.list[[all.db[i]]] <- names(list.source)[unlist(lapply(list.source, function(x) all.db[i] <!-- %in% x))] -->
}

# upset plot
plt.upset <- upset.Plot(gene.sets = db.list, row.title = "", column.title = "")

LR.df <- LR.db
LR.list <- db.list
LR.upset.plot <- plt.upset
LR.db <- list(
  LR.df = LR.df,
  LR.list = LR.list,
  LR.upset.plot = LR.upset.plot
)

output.dir <- "C:/Users/Owner/Dropbox/PDF Projects - JM/R Packages/scMiko/data/"
save(LR.db, file=getLoadPath("LR.db.rda", output.dir))
}

Format

A list containing LR database

Author

Magali Aguilera Uribe

Examples

data(LR.db)