#' Create TG dictionary
#'
#' Create a dictionary to transcriptogramer package
#'
#' @param ensembleGeneId vector of ensemble GeneId that have counts.
#' @param dataset ENSEMBL dataset name. A dataset name can be retrieved with list_datasets() function.
#'
#' @details
#'
#' @return
#' @export
#'
#' @examples
create_tg_dict <- function(ensembleGeneId, dataset = "hsapiens_gene_ensembl") {
if (missing("ensembleGeneId")){
stop("A ensemble GeneId list must be provided\n")
}
att <- c("ensembl_gene_id", "ensembl_peptide_id")
platform<-"none"
db <- "main"
dic_tg <- data.frame(PROBE=ensembleGeneId, stringsAsFactors = F)
bmList <- get_annotation(dataset = "hsapiens_gene_ensembl",att = c("ensembl_gene_id", "ensembl_peptide_id"))
#Discard any empty reference of ensembl_peptide_id
bmList<-bmList[grep("ENSP",bmList[,"ensembl_peptide_id"]),]
#Dictionary with gene ID (PROBE) and ensemble ID (ENSP)
dic_tg<-merge(dic_tg,bmList,
by.x="PROBE",by.y = "ensembl_gene_id")
colnames(dic_tg)<-c("PROBE","ENSP")
#the prefix 9606. will be needed later
dic_tg$ENSP<-gsub("ENSP","9606.ENSP",
dic_tg$ENSP,fixed = T)
return(dic_tg)
}
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