#' Converting mouse gene symbol to human gene symbol of expression set.
#'
#' @param eset expression matrix or data frame
#' @param source default is ensembl, if an error is reported, set parameter to `local` and mus_human_gene_symbol will be use to convert gene symbols
#' @param is_matrix default is T, if not, column_of_symbol must be se
#' @param column_of_symbol default is null
#'
#' @return
#' @export
#'
#' @examples
#'
mouse2human_eset<-function(eset, source = "ensembl", is_matrix = T, column_of_symbol = NULL, verbose = FALSE){
if(is_matrix){
genes<-rownames(eset)
}else{
eset<-remove_duplicate_genes(eset = eset, column_of_symbol = column_of_symbol)
genes<-rownames(eset)
}
if(source=="ensembl"){
require("biomaRt")
ensembl = biomaRt:: useEnsembl(biomart="ensembl")
if(verbose) print(head(listDatasets(ensembl)))
# Basic function to convert mouse to human gene names
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
probe_data = getLDS(attributes = c("mgi_symbol"),
filters = "mgi_symbol",
values = genes ,
mart = mouse,
attributesL = c("hgnc_symbol"),
martL = human,
uniqueRows=T)
colnames(probe_data)<-c("gene_symbol_mus", "gene_symbol_human")
}else if(source=="local"){
probe_data<-mus_human_gene_symbol
}
eset<-anno_eset(eset = eset, annotation = probe_data, symbol = "gene_symbol_human", probe = "gene_symbol_mus",method = "mean")
return(eset)
}
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