R/makeGOTable.R

In tschauer/HelpersforDESeq2: This is a collection of helper functions for DESeq2

#' makeGOTable
#'
#' make a Gene Ontology enrichment table on DESeq2 results using topGO package
#' @export




makeGOTable <- function(all_genes,
                        shown_terms = 20,
                        min_signficant = 5,
                        select_ontology = "BP",
                        select_organism = "org.Mm.eg.db",
                        select_ID = "SYMBOL"){


        tgd <- new( "topGOdata",
                    ontology = select_ontology,
                    allGenes = all_genes,
                    nodeSize=5,
                    annot=annFUN.org,
                    mapping = select_organism,
                    ID =  select_ID)

        resultTopGO <- topGO::runTest(tgd, algorithm = "classic", statistic = "Fisher")


        df <- topGO::GenTable( tgd,
                               Fisher.classic = resultTopGO,
                               orderBy = "Fisher.classic" , topNodes = 100)


        df <- df[df$Significant >= min_signficant,]
        df <- head(df, shown_terms)
        df$`Sign/Exp` <- df$Significant / df$Expected

        gene_list <- topGO::genesInTerm(object = tgd, whichGO = df$GO.ID)
        gene_names <- unlist(lapply(gene_list, FUN = function(x){paste(x[x %in% (names(all_genes)[all_genes == 1])], collapse = "/")}))


        df <- merge(df, data.frame(gene_names), by.x="GO.ID", by.y = "row.names")

        rownames(df) <- df$GO.ID
        df <- df[,-1]
        df$Fisher.classic <- gsub("< 1e-30","1e-30",df$Fisher.classic)
        df$Fisher.classic <- as.numeric(df$Fisher.classic)
        df <- df[order(df$Fisher.classic),]

        return(df)
}




########################################################  first letters up or down    ########################################################



firstup <- function(x) {
        substr(x, 1, 1) <- toupper(substr(x, 1, 1))
        x
}


firstdown <- function(x) {
        substr(x, 1, 1) <- tolower(substr(x, 1, 1))
        x
}