mirna.enrich: Main function of miRNAEnrich package. Computes miRNA...

In komalsrathi/miRNAEnrich: Enrichment of miRNA

Usage

mirna.enrich(mir.db = c("targetscandb", "microRNA"), org = c("mmu", "hsa"), fg, bg, col = "Symbol", plot = TRUE, cutoff)

Arguments

mir.db
org
fg
bg
col
plot
cutoff

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 (mir.db = c("targetscandb", "microRNA"), org = c("mmu", 
    "hsa"), fg, bg, col = "Symbol", plot = TRUE, cutoff) 
{
    require("plyr")
    if (!((org == "mmu" | org == "hsa") & (mir.db == "targetscandb" | 
        mir.db == "microRNA"))) {
        stop("Allowed values for org = hsa or mmu\n Allowed values for mir.db = targetscandb or microRNA")
    }
    mir.db = get(paste(mir.db, org, sep = "."))
    if (is.na(cutoff)) {
        mir.db = mir.db
    }
    else if ("context..score" %in% colnames(mir.db)) {
        mir.db = mir.db[which(mir.db$context..score <= cutoff | 
            is.na(mir.db$context..score)), ]
    }
    else if ("mirsvr_score" %in% colnames(mir.db)) {
        mir.db = mir.db[which(mir.db$mirsvr_score <= cutoff | 
            is.na(mir.db$mirsvr_score)), ]
    }
    ftest.results = data.frame()
    ftest.results = rbind(ftest.results, ddply(.data = mir.db, 
        .variables = "miRNA", .fun = function(x) ftest.fun(x, 
            fg = fg, bg = bg, col = col)))
    ftest.results$pvalue.adj = p.adjust(p = ftest.results$pvalue, 
        method = "fdr")
    ftest.results = ftest.results[order(ftest.results$pvalue), 
        ]
    if (plot) {
        require("ggplot2")
        ftest.results.sub = ftest.results[which(ftest.results$pvalue.adj < 
            0.05), ]
        ftest.results.sub$miRNA = factor(ftest.results.sub$miRNA, 
            levels = rev(ftest.results.sub$miRNA))
        p <- ggplot(data = ftest.results.sub, aes(x = miRNA, 
            y = Foreground.Present, fill = pvalue.adj)) + geom_bar(stat = "identity") + 
            coord_flip() + theme(axis.text.y = element_text(color = "black", 
            size = 12), axis.text.x = element_text(color = "black", 
            size = 12), legend.text = element_text(color = "black", 
            size = 12), legend.title = element_text(color = "black", 
            size = 12), axis.title.x = element_text(color = "black", 
            size = 14), axis.title.y = element_text(color = "black", 
            size = 14), plot.title = element_text(color = "black", 
            size = 16)) + ggtitle("Enriched miRNA P.Adj<0.05\n") + 
            ylab("\nGenes in Foreground") + xlab("miRNA\n")
        print(p)
    }
    return(ftest.results)
  }

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