Task3a - illumina annotation to output: gene, feature and relation to…

R/annotateDMR.R

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+#' Function to annotate
+#' 
+#' This function annotates a methylated region
+#' TxDbannotation package is required
+#' @param data DataFrame-like object.
+#' @param db Database to use for annotation. E.g: IlluminaHumanMethylationEPICanno.ilm10b2.hg19.
+#' @param epi_col CpG ids, should be rownames in database.
+#' @param gene_col Column name from where to extract gene names. Default: 'GencodeBasicV12_NAME'.
+#' @param feat_col Column name from where to extract CpG feature groups. Default:  'Regulatory_Feature_Group'.
+#' @param relat_col Column name from where to extract relation to island info. Default:  'Relation_to_Island'.
+#' @return DataFrame-like object annotated.
+#' @export
+annotate_CpG <- function(data, db, epi_col='CpG_ids', gene_col='GencodeBasicV12_NAME', feat_col='Regulatory_Feature_Group', relat_col='Relation_to_Island'){
+	message('Annotating:')
+	anno <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)
+	epids_list <- data[[epi_col]]
+	message(paste('-', gene_col))
+	annotated_genes <- lapply(epids_list, function(x){
+		paste(anno[x,][[gene_col]], collapse='///')
+	})
+	message(paste('-', feat_col))
+	annotated_regions <- lapply(epids_list, function(x){
+		paste(anno[x,][[feat_col]], collapse='///')
+	})
+	message(paste('-', relat_col))
+	annotated_relation <- lapply(epids_list, function(x){
+		paste(anno[x,][[relat_col]], collapse='///')
+	})
+
+
+	data[[gene_col]] <- annotated_genes
+	data[[feat_col]] <- annotated_regions
+	data[[relat_col]] <- annotated_relation
+	return(data)
+}