getTargets: This function is used by getOverlappingTargets function to...

In komalsrathi/miRNAEnrich: Enrichment of miRNA

Usage

getTargets(db, table, mir.fam)

Arguments

db
table
mir.fam

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (db, table, mir.fam) 
{
    require("data.table")
    db = merge(db, mir.fam[, c(1, 4)], by.x = "miRNA", by.y = "miRBaseID")
    db = as.data.table(db)
    var1 <- unique(as.character(db[miRNA %in% table$mir1, Gene.Symbol]))
    var2 <- unique(as.character(db[miRNA %in% table$mir2, Gene.Symbol]))
    overlap <- length(intersect(var1, var2))
    var1 <- length(var1)
    var2 <- length(var2)
    miRFamily.mir1 <- unique(as.character(db[miRNA %in% table$mir1, 
        miRFamily]))
    miRFamily.mir2 <- unique(as.character(db[miRNA %in% table$mir2, 
        miRFamily]))
    res <- data.frame(miRFamily.mir1 = miRFamily.mir1, mir1.targets = var1, 
        miRFamily.mir2 = miRFamily.mir2, mir2.targets = var2, 
        overlap = overlap, mir1.targets.perc = round(overlap/var1 * 
            100, 2), mir2.targets.perc = round(overlap/var2 * 
            100, 2))
    return(res)
  }

komalsrathi/miRNAEnrich documentation built on May 20, 2019, 12:55 p.m.