R/getBM_annotation.R

In anschue/toxprofileR: Functions for Retrieving Dynamic Toxicogenomic Fingerprints

#' get biomaRt annotaiton
#'
#' @param values IDs
#' @param filter Type of IDs (default: "ensembl_gene_id")
#' @param mart a biomaRt object
#'
#' @return a dataframe with selected biomaRt annotations
#' @export
#'
getBM_annotation <-
  function(values = mapFinal_reduced$ensembl_gene_id,
             filter = "ensembl_gene_id",
             mart) {
    library("biomaRt")

    if (filter != "ensembl_gene_id") {
      BM_ensembl <-
        biomaRt::getBM(
          attributes = unique(
            c(
              filter,
              "ensembl_gene_id"
            )
          ),
          filters = filter,
          values = values,
          mart = mart,
          uniqueRows = T
        )


      values <- BM_ensembl$ensembl_gene_id
    }


    BM_IDS <-
      biomaRt::getBM(
        attributes =
          c(
            "ensembl_gene_id",
            "external_gene_name",
            "description",
            "hsapiens_homolog_associated_gene_name"
          ),
        filters = "ensembl_gene_id",
        values = values,
        mart = mart,
        uniqueRows = T
      )

    BM_IDS <-
      aggregate.data.frame(
        BM_IDS,
        by = list(BM_IDS[, "ensembl_gene_id"]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]

    BM_GO <-
      biomaRt::getBM(
        attributes = c("ensembl_gene_id", "name_1006"),
        filters = "ensembl_gene_id",
        values = values,
        mart = mart,
        uniqueRows = T
      )

    BM_GO <-
      aggregate.data.frame(
        BM_GO,
        by = list(BM_GO[, "ensembl_gene_id"]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]


    BM_interpro <-
      biomaRt::getBM(
        attributes = c("ensembl_gene_id", "interpro_description"),
        filters = "ensembl_gene_id",
        values = values,
        mart = mart,
        uniqueRows = T
      )

    BM_interpro <-
      aggregate.data.frame(
        BM_interpro,
        by = list(BM_interpro[, "ensembl_gene_id"]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]

    BM_phenotype <-
      biomaRt::getBM(
        attributes = c("ensembl_gene_id", "phenotype_description"),
        filters = "ensembl_gene_id",
        values = values,
        mart = mart,
        uniqueRows = T
      )

    BM_phenotype <-
      aggregate.data.frame(
        BM_phenotype,
        by = list(BM_phenotype[, "ensembl_gene_id"]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]

    BM_genetype <-
      biomaRt::getBM(
        attributes = c("ensembl_gene_id", "gene_biotype"),
        filters = "ensembl_gene_id",
        values = values,
        mart = mart,
        uniqueRows = T
      )

    BM_genetype <-
      aggregate.data.frame(
        BM_genetype,
        by = list(BM_genetype[, "ensembl_gene_id"]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]


    BM_all <-
      Reduce(
        function(...)
          merge(..., by = "ensembl_gene_id", all = TRUE),
        list(BM_IDS, BM_GO, BM_interpro, BM_genetype, BM_phenotype)
      )

    if (filter != "ensembl_gene_id") {
      BM_all <- merge(BM_ensembl, BM_all, by = "ensembl_gene_id", all = TRUE)
      BM_all <- aggregate.data.frame(
        BM_all,
        by = list(BM_all[, filter]),
        FUN = function(x) {
          paste(unique(x))
        }
      )[, -1]
    }

    return(BM_all)
  }